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Jaguar User Manual - The Friesner Group

1. 143 7 3 GVB RCI Wave Functions sess 147 7 4 Pseudospectral Local MP2 Techniques sess 149 7 5 Density Functional Theory sse 152 Chapter 8 The Jaguar Input File 155 8 1 General Description of the Input Pie 155 8 1 1 IpputiElle EE 155 8 1 2 Sections Describing the Molecule and Calculation 156 8 2 The zmat zmat2 and zmat3 Sections 0 0nonnonaeoannaenannannaenaninnneninnennnnnee 158 8 3 The zvar Zvar2 and zvar3 Gechons 159 8 4 The coord and connect Sections sss 160 8 4 1 Constrained Coordinates iecit eee ene Pe EARS ISSN Aiea 161 8 4 2 Specifying Bonds for Internal Coordinates with a connect Section 163 Jaguar 7 0 User Manual vii Contents viii 8 5 The EE 163 8 51 Units Keywords cos re rp nr C TEE RUE EMO RE eine 163 8 5 2 Covalent Bonding Keyword rrt ro rae retro Fs ENEE SES EeE 164 8 5 3 Molecular State Keywords Charge and Multiplicity 164 8 5 4 Atomic Mass Keyword eil siepe ede bue e ie adl es RE EE 165 8 5 5 Symmetry Related Keywortds 2 breite estes idet b rode edit Abo decia 165 8 5 6 GVB and Lewis Dot Structure Keywords esee 165 3 5 7 UMPA CUI EET 167 8 5 8 DFT Keywords sies etr eibi I Ed HL IS LIES aR 169 8 5 9 GIS ang PDDET KeyWords 3 5
2. eene 262 Jaguar 7 0 User Manual Contents Chapter 10 Running JOD aie dicato diia dictis ucc dus 263 10 1 The jaguar lu WEE 263 1031 1 Selecting an Execution Flost occ t trennt eot rts trie rni ru ger 265 10 1 2 Selecting Particular Jaguar Executables AA 266 10 1 3 Running a Jaguar Job From the Command Line s esssseesseseenerrernsrreresrnere 266 1031 4 Killing a Jaguar Job iati ront t toten ated e PE Fett bake RR dean 268 10 1 5 Converting File Formats tutari roris tetti teret ttd ie th Fea testa ient dean 269 10 2 Running Multiple Jobs jaguar batch sse 272 10 2 1 Batch Input File FOrtflal c iieri Egide oc oed nupt sc Hur SE een 272 10 2 2 Bunning jaguar E 276 10 2 3 Batchi Input File EXaimiples seaside aii nish deti ia aes 277 10 291 Pipelined JODS isc m 278 10 2 3 2 Running Jobs from Input in a Specified Directory 278 10 2 4 Using Python Scripts with jaguar baich sese 279 REN Meo Viger 279 10 2 4 2 e ere EE DEE 280 Chapter 11 Troubles e DEus easi peaks uni Fc DH Fr D 283 11 1 Problems Getting Started sse 283 11 1 1 The SCHRODINGER Environment Variable sese 283 11 1 2 Including the jaguar Command in Your Pat 284 11 1 3 Problems Starting MaG6SItO rin sete stes be ert bab eH HR Seco SEES ADEM D Rd ER 285 11 1 4 Problems R
3. eee 124 125 GAMESS input file s 207 GAUSSIAN input gau file 139 key Words ainnise 206 207 Index XY EE 125 first solvation shell correction factor key word 186 SM6 corrections sese 51 Fock matrix in DIIS error vector 96 129 keywords for output of 205 208 new estimate from DIIS scheme 95 128 pseudospectral assembly of 141 143 UP atin asics cet E ra t Re 95 128 updating keyword sues 195 forces keywords 177 178 180 formal Charge wisi iere eiii 220 fragments RIS 227 frequencies for 192 227 Ereg E EE 234 frequencies 58 63 analytic eegen 58 fragment ise 192 227 keywords voce 180 191 OUEDpUE E 114 116 Tee Ee eg eer 60 visualizing in Maestro ssse 60 visualizing with Molden 62 frequency related properties Maestro settings eee 62 63 oin M e EE tens 114 116 functionals see density functional theory DFT G GAMESS input files keyword for 207 OPON TOT eegen niter teneri 124 GAUSSIAN Hessian format 228 orbital output in format for 126 209 GAUSSIAN basis set file gbs keyword for generatio of toaster te e espe 207 Gaussian function list in outpu
4. 204 listing in out 114 Mulliken populations for 113 number of 30 92 243 e EE 117 120 type as listed in output 126 uncontracted 00 0 eceeesseeeeessseeeeees 117 118 hoe Ea 30 35 conversion to Jaguar format 241 diffuse functions 30 192 238 file containing eee 237 241 for individual atoms 222 for initial guess 132 229 242 for SM6 solvation sss 52 keywords listed in output TAGS e polarization functions 30 35 192 238 specifying for GAUSSIAN input 140 207 with ECP in output esee 117 basis set superposition error 14 40 42 150 batch input file example acte cei riirii 277 format ces uoieinetiieeiceeeet 272 276 batch jobs jaguar batch command for 272 277 inni c 211 running from Maestro 24 27 DatCh Senf iret Orten 272 loisir 26 selecting in Maestro 25 BFGS method for Hessian updating keyword 180 BIOGRAF hes files format 228 bond angles freezino all ite meme freezing for geometry optimization 71 72 160 WA ZAI d output keyword bond dissociation assigning GVB pairs for 136 bond lengths freezing allzu sienne t 179 Jaguar 7 0 User Manual 333 Index 33
5. Molecule Theory scr Properties Solvation Output Level of theory DFT Density Functional Theory DFT 7 Spin unrestricted W Excited state TDDFT Number of excited states 1 Maximum TDDFT iterations 32 Grid density Medium Functionals Hybrid B3LYP wv Gradient corrected BLYP a v LDA SVWN Job B3LYP 6 31G Single Point Energy Frequencies Start Read Write Edit Reset Close Help Figure 3 2 The Theory tab showing DFT controls The Grid density menu determines the grid for DFT calculations By default DFT calculations use grids with a medium point density but finer density grids are also available You can choose between Medium Fine or Maximum grid density If you read an input file that contained some other grid density the grid density is set to Other otherwise this option is unavailable If you choose a grid density from this menu the previous grid density specifica tion is replaced 7 Keywords gdftmed 10 gdftfine 11 and gdftgrad 12 in the gen section 8 Keywords gdftmed gdftfine and gdftgrad 13 in the gen section 9 Keywords gdftmed gdftfine gdftgrad 14 in the gen section Jaguar 7 0 User Manual Chapter 3 Options The most commonly used functionals can be selected from the option menus in the Functionals section There are three classes of functionals available
6. eee 300 installation 5 5 retentis 291 Linux installation eese 295 SGI installation eee 292 partial charges from ESP fit uen recte 52 Maike ctn uerunt 54 path specifying order of programs 233 235 PDE program oem dieto ees 234 output from geometry optimizations 109 per iteration output options 207 208 physical constants and conversion factors keyword we 194 Pipek Mezey localization 48 in LMP2 calculations eee 41 keywords 168 200 orbital printing eene 125 pK calculations conformational flexibility 307 empirical corrections ees 306 equivalent sites 307 308 geometry optimization eee 304 initial geometry esee 317 input files iei terni 313 e OT 315 multiple protonation sites 307 309 313 PUDDING 3c cacsedesuvoseeisassaeviveseasssdassexteees 311 314 single point energies ss 305 solvation free energy sse 305 mL 304 pK prediction module Installing ee tra tercie 311 parameterized functional groups 310 training set results 309 plot data generating sess 63 214 POE Parallel Operating Environment options automatically set
7. 302 version required sess 300 point charges input file section for 230 231 Poisson Boltzmann equations 49 Poisson Boltzmann solver 48 51 OUtpUt ITO eet rre rero pere 103 polar program eret Irene 234 Index polarizability EEN 55 keywords ertt 189 190 Maestro options eene 55 57 polarization free energy sese 107 population analysis Eo n EEN af MU KEN ain Sven Rte 54 see also Mulliken population analysis POSE PLOBTAIM sis eese ether trie 234 Output ATOM 2 65 nnns 103 potential energy surface scan 80 84 potential electrostatic output on a gd 190 apre E 63 Powell update method keyword 180 Dre prOBratu eei tr toner peni 233 output from sese 92 100 102 pressure for thermochemical calculations keyword option OUUp Ut E P RFO level shifting keyword for 181 probe program protette erento 233 probe radius of solvent 50 327 processors determining optimum number 302 selecting number of sess 267 product geometry for IRC caleulattons 86 in transition state search 75 specifying in input file 159 specifying in Maestro 76 product installation esee
8. 25 77166631229 32 84704880440 7 07538249211 Hamiltonian 2 6 02807668738 6 99023521309 0 96215852571 02990515066 6 99271668375 0 96281153309 03711925295 0 06576591758 0 02864666463 03701395705 0 06563507622 0 02862111917 Hamiltonian 3 Hamiltonian 4 Hamiltonian 5 oon List of Intra Pair K Energies 0 03983705429 0 03981442075 Sum of Intra Pair K Energy 0 07965147505 GVB pair information first natural orbital second natural orbital Eeer E EE ci energy pair orb ham shl ci coeff orb ham shl ci coeff overlap lowering 1 4 2 2 0 995433818 6 4 4 0 095454256 0 824997160 0 020103338 2 5 3 3 0 995443725 7 5 5 0 095350881 0 825171705 0 020091467 Jaguar 7 0 User Manual Chapter 5 Output SCFE SCF energy GVB 76 06328826029 hartrees iterations 8 Each row in the GVB pair information table lists the pair number the orbital number after all core and open orbitals have been assigned numbers Hamiltonian number after the core Hamiltonian and any open Hamiltonians have been assigned numbers and shell number after the core shell and any open shell have been assigned numbers corresponding to each natural orbital and CI coefficient corresponding to each GVB natural orbital in the pair Next the overlap between the two corresponding non orthogonal orbitals for that pair is listed followed by the CI energy lowering which is a guide to the energy change resulting from the inclusion
9. sssss memory keywords niet troubleshooting related to memory disk and i o information key WOI ane nunm ian ater 204 output opton ikkisin 122 minimum energy path MEP calculations 84 Molden orbitals file mo1 keyword for 207 molecular charge key WOT er eege ier retinentes 164 Maestro setting see 18 molecular properties see properties molecular state keywords 164 Index molecular structure see geometry input geometry optimization Molecule boeuf en eret 31 Moller Plesset second order perturbation theory see LMP2 Monitor panel 5 c dtedecietieaeeeistee 5 24 MP2 see LMP2 hier 167 MPI flags setting erret 302 mnpzch utility i terreas 297 MOM basis set file bas keyword 207 Mulliken population analysis 54 for basis functions sse 54 keyword eset trennen 189 output from serere 113 114 output of multipole moments from 114 recalculating multipole moments from 54 55 Mulliken spin populatons s ssssssseseeeeeeeeeeeeee 54 multiple Jaguar jobs running ATOM Maestro ote eee with jaguar batch multiplicity key WOE iecore noter tte orn 164 setting in Maestro 18 multipole moments calculating eet 55 136 from electrostatic potential fitting 54 55 111 from Mulliken population analysis 54 55 114 KEY WOT
10. b3pw91 Exchange exact HF Slater local functional 34 Becke 1988 non local gradient correction 37 correlation Perdew Wang 1991 local and GGA II nonlocal func tional 36 b3p86 Exchange exact HF Slater local exchange functional 34 Becke 1988 nonlocal gradient correction 37 correlation Vosko Wilk Nusair VWN local functional 35 and Perdew 1986 nonlocal gradient correction 40 bhandh 50 exact HF exchange 50 Slater local exchange functional 34 bhandhlyp Exchange 50 exact HF exchange 50 Slater local exchange functional 34 correlation Lee Yang Parr local and nonlocal functional 38 b97 1 Reparametrization of Becke s 1997 hybrid functional 42 by Hamprecht Cohen Tozer and Handy 45 b98 Becke s 1998 hybrid functional including the Laplacian of the density and kinetic energy density terms as well as gradient terms 43 sb98 Schmider and Becke reparametrization of Becke s 1998 functional 44 mpwlpw91 Hybrid functional including modification of Perdew Wang gradient correction exchange functional by Adamo and Barone 48 Exchange 25 exact HF exchange 75 Slater local functional 34 and Perdew Wang 1991 gradient cor rection functional 36 correlation Perdew Wang 1991 GGA II local and nonlo cal functionals 36 mpwlk Reoptimization of mPW1PW91 functional parameter for prediction of barrier heights by Lynch Fast Harris and Truhlar 49 pwb6k Reoptimization of MPWBIK functional fo
11. sss 18 27 1 Quick Geometry Oplimlizationi Eeer 18 2 7 2 SYMMEWIZALON sin in sire teet teri Pede e teen Renee IEEE eden centers 19 2 8 Writlfig RUE 21 2 9 Runnin Jobs ios eet deg I RIO ROLE DR IER 22 29 1 Output Della EE 22 2 9 2 Job Submission EES es RESEARCH 23 2 9 3 Staring and Monitoring JOBS i recte rien tnb mortars mi 24 Jaguar 7 0 User Manual Contents 2 10 Running Jaguar Batch Jobs 24 Cake 27 2 12 J2 Theory Calculations perpe A NEE 27 2 13 Binding Energies of Hydrogen Bonded Complexes 28 Chapter 3 ee NT 29 3 1 Molecule le CG 29 ENEE 30 3 3 Density Functional Theory DFT Settings sse 35 3 4 Hartree Fock and CIS Settings A 40 3 5 Local MP2 Settings EE 40 3 6 Generalized Valence Bond GVB Gettinge sss 43 3 7 GVB EMP2 e DE 44 3 0 SCF SGUINGS e 45 3 8 1 Accuracy Level adeb aei tete ie deii ia nies os EN ese I dea Re hada 45 3 8 2 ENEE 45 3 8 3 Convergence Methods eese HE Rer eed er naan nailer 47 3 9 4 Orbital Ireatmigfil EE 48 3 9 Solvation Settings eie ri HEIDE ERU DID MIERR IIO N 48 3 9 1 Poisson Boltzmann Solvation Model eene 48 3 9 2 Solvation MOGelB edes eiie eatin aati eer EPIS hee 51 KW EE 52 3 10 1 Charges from Electrostatic Potential Fitting sseseesrssreersrsrrrrrerrernrresrnrneenee 52 3 10 2 Mulliken Population Analysis otio tratar
12. To use the file in a Jaguar calculation you must add a line in the form BASISFILE filename to the input file for the job You can specify a file on another host or under another account name on that host by listing the file name in the format host fullpath or user amp host fullpath To make it easier to add basis sets to Jaguar a script called makejbasis has been provided that converts basis sets in GAUSSIAN 94 format as downloaded from the PNNL web site into Jaguar format The basis set download page of the PNNL web site is at http www emsl pnl gov forms basisform html When you download the basis sets you must save the data in text format not HTML format The syntax of the makejbasis command is Jaguar 7 0 User Manual 241 Chapter 9 Other Jaguar Files 242 S SCHRODINGER utilities makejbasis input filename output filename where input filename is the name of the GAUSSIAN 94 format data file and output filename is the name of the Jaguar format basis set file The script is a Perl script If Perl is not installed in usr bin you can run this script by prefacing the command with per1 Because Jaguar currently cannot use g or higher basis functions basis functions with angular momentum g or higher are removed from the basis set and a warning is displayed If a basis set contains an ECP with h or higher potential projectors with angular momentum g or higher the entire basis set for that element is not c
13. 232 pz 233 235 point h uiii 230 231 zmat zmat2 mat 158 159 ZVAL 158 zvar Zvar2 zwar 159 160 input of molecular structure see geometry input installation directory 283 284 integrals one clectron 93 integrals two electron contributions to energy s s s 98 pseudospectral approximation to 143 internal coordinates in optimization keyword for 178 specifying with connect section 160 163 specifying with coord section 160 163 internal energy calculations 62 63 115 191 intrinsic reaction coordinate IRC calculations ioannas 84 184 IR intensities see infrared intensities Td PIO STAN ect nh a Er EI eb 234 irb progra n rr rr ne eh un 234 UE te diu Rute 85 isotopes keyword atomic section 221 keyword gen section sess 165 iterations maximum number geometry optimization 69 136 178 e 45 134 194 J J2 theory calculatons sess 2 jagconvert utility sse 272 jaguar command 263 272 including in DAT 284 jaguar babel 269 272 jaguar baths enee 272 277 jag ar help cen ete n 264 jaguar jobs aec hte entree 264 RUE neant 268 jaguar machid sseeeeseeee 264 Jaguar platfOotm ui eeee eene 264 jaguar results eite eee 87 92 jaguar E 266 268 SET E 264 Jaguar
14. 8 T COST ELO T ICST L60C 9eX Fc cat ce as IS US OS UI epp 8r 8SV Lv Pd Op QW Sp PHL klot Cr aN IP JZ Op A GCHg Co LE ILOT S60 C COLT SITT Orc TOLT ISET SPELT LIFT 9er7 967 T OST TIST CLOT L8S T LOT OOL T 9061 TA OCH SEIS v SV CC CID IEJUZ O nO 6C IN 86 00 LTA OTUN SCHO YTA ETIL GC ITee OTCA ol 8961 896 T OLOT LYTT LITT 80 C 80 C 80 C Iv 8I D LIS O9I d STS rvI IV el SW CI EN TI DELL 9EL T COLT I 8 T 6r6 T CHOC LE T 9ccTI N OlH 60O 8N LO 9d ed FI ISUI Lol 9H H I seDieuo pay dS3 jenuejod orejsojjoojo Jo uogejnojeo ui pesn suosDuy ul DEI SjeeM JOP UBA erg ojqe 223 Jaguar 7 0 User Manual The Jaguar Input File Chapter 8 SSTT SPUT PLUT ESET LET LLET OCFT O9 TL LAYI VEST S8S T OLST TOLT ISS T 6S9CC tdg 8 dd 78ILL IS 2H min od SLIT LL SO 9L eW SLIM FL LJH CL I Le ed oe SS TOTT 0scc SETT OTT 96l c TETT ver T PLOT OSPI v9 TL ISP TL 16671 908 TL 88 TL COCT 97 TL ICT Lo 9X PSII ES IL cc as IS US Ou opp 8t 9V LEID Op UN Sb hW Pla Cla CP QN IFIZ OP A 6 S SEI LE ILOT S60 C COLT SITT OPET TOLT ISET BLT LIT 9er T 987p OSHT TIS T CELO T Z88 T LYST OOL T 9061 IM OCI St 9S vt sSV ECOD Ct D IE UZ Ot nOD 6C IN 8c 0D LTA 9c UIN SCHO FA tC lL TEOS ITED OTA ol veel
15. For the first hyperpolarizability three sums are reported which are defined by the following expression B Bos Byyy Bazz where q can be x y or z The average hyperpolarizability D is defined by B ZB en 2B HB where p is the dipole moment The average second hyperpolarizability y is defined by y 22 agn P 4 Jaguar 7 0 User Manual Chapter 5 Output where p and q run over the three coordinates x y and z 5 3 7 3 Electron Density If you choose to calculate the electron density the output from the program elden appears below the SCF output The output lists the number of grid points used for the electron density calculation and the total number of electrons found over the grid The main output file does not include the charges and grid points for the calculation that information can be found in the output file jobname chdens where jobname in is the input file for the Jaguar job The file jobname chdens lists the Cartesian coordinates and the electron density in au respectively for each grid point 5 3 7 4 Mulliken Populations If you calculate Mulliken populations by atom the atomic charges and their sum is given under the heading Atomic charges from Mulliken population analysis If you calculate them by basis function the atomic charge output is preceded by a section labeled Mulliken population for basis functions listing the atom label basis function index basis function type
16. Reset Resets all the settings in the Jaguar panel to the default state for the selected task Close Closes the Jaguar panel Help Opens the help viewer at the topic for the currently displayed tab 2 3 The Edit Job Dialog Box While most of the common settings for Jaguar jobs can be made in the Jaguar panel you might need to make changes to the settings add keywords to the input file for options that are not available from the Jaguar panel or make changes to the geometry You can make these changes in the Edit Job dialog box which you open by clicking Edit in the Jaguar panel Apart from standard editing tools this dialog box has special tools for editing Jaguar input files The basic editing tools are contained in the File and Edit menus The File menu allows you to save the current state of the input file to disk Write and to cancel all your changes without closing the dialog box Revert The Edit menu provides Cut Copy and Paste options for cutting and pasting within Maestro but you cannot use these to copy text from another applica tion To copy and paste text from another application or from Maestro highlight the text then middle click where you want the text to be pasted The text in the paste buffer is saved when you close the dialog box so you can copy text between input files Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro The Edit Job dialog box has two editing modes Input File and St
17. The torsional angle is the angle between the plane formed by the first three atoms in this case N1 C2 C3 and the plane formed by the last three atoms in this case C2 C3 O4 Looking from the second to the third atom C2 to C3 the sign of the angle is positive if the angle is traced in a clockwise direction from the first plane to the second plane and negative if the angle is traced counterclockwise An alternative for specifying the fourth atom s position is to use a second bond angle instead of a torsional angle To specify another bond angle add 1 or 1 to the end of the line The second bond angle is the angle between the first second and fourth atoms in the example above the O4 C3 NI angle Since there are two possible positions for the atom which meet the angle specifications the position is defined by the scalar triple product r 5 r5 x r34 where r r r is the vector pointing from atom j to atom i If this product is positive the value at the end of the line should be 1 If it is negative the value should be 1 You should use torsional angles Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro instead of second bond angles if you want to perform a constrained geometry optimization however since Jaguar cannot interpret any constraints on bond lengths or angles for geome tries containing second bond angles All additional lines of the Z matrix should have the same form as the fourth line The
18. 346 versions of Jaguar VS Bs E 266 Sel cting unen meo tease 267 Vibration panel rettet 62 vibrational frequencies esses 58 keywords for Se Sei visualizing in Maestro ssse 60 visualizing with Molden 62 VAT AL EAUO EE 204 virtual orbitals keyword for number printed 208 number Drimnted usse 96 126 Jaguar 7 0 User Manual W working directory eere 213 X XYZ file xyz output option 125 Z Zero point energies 62 63 115 191 Z matrix Tomat 11 14 158 160 dummy atoms In 13 variables mm 13 14 159 160 Keyword Index Numerics Po m 221 B babel eee eR 201 204 UE 201 204 DAS OSS an tee IE 229 LTC 192 227 C OU E 188 190 dconvci denspc epsout Idtemp sene eerte 196 formal ect tlie ENEE 221 ue 227 r gfrag oco pod binos 192 227 G gcliaree eene te eres 190 212 253 DICT E 212 253 gconv1 gconv7 ssseseeee 183 pdftephi eigene o 210 gdftder2 eie hte 210 gditfine E 210 gdftgrad 5 210 253 gdftmed E 210 253 geldens nens 189 190 212 253 ty rl n 212 253 porad e 212 253 UE EE 197 cavity ooi dre REGES 186 MCA 188 Ichange 5
19. 4 G CDS liq cavity dispersion solvent structure free energy 1 154 kcal mol 5 G P CDS liq G P liq G CDS liq 2 4 4 941 kcal mol 6 G S liq free energy of system 1 5 95 823961858 a u 7 DeltaE EN elect nuc reorganization energy of solute molecule 7 1 0 200 kcal mol 8 DeltaG ENP elect nuc pol free energy of solvation 8 3 0 3 586 kcal mol 9 DeltaG S free energy of solvation 9 6 0 4 741 kcal mol The value listed in the first line E EN g is the total electronic and nuclear energy in the gas phase as reported for the gas phase SCF calculation It is followed by the internal solute energy in the solution phase E EN liq as reported for the solution phase SCF calculation Next is the polarization free energy of solvation G P liq that results from using the converged solution phase partial atomic charges The sum of the solute s internal energy in the solution phase E EN liq and the polarization free energy G P liq is listed in the next row this sum is called G ENP 1iq followed by the first solvation shell contribution to the solvation free energy G CDS liq The next line lists the sum G P lig G CDS liq which is called G P CDS liq After G P CDS liq is listed the output shows the total solution phase free energy of the system GS liq which is the sum of E EN liq and G P CDS liq The values for Delta EN DeltaG ENP an
20. 51 Chapter 3 Options 52 contained in SM6 were developed using rigid molecular geometries optimized in the gas phase doing this does not lead to a significant reduction in the accuracy of the results for most systems Additionally it has been shown that the solvation free energies obtained using SM6 are typically not very sensitive to the level of theory used to compute the molecular geometry so that a molecular geometry obtained from any reasonable gas phase or solution phase calcu lation can be used as input for an SM6 calculation To run an SM6 solvation calculation choose SM6 from the Solvent model option menu in the Solvation tab The solvent is automatically set to Water which is the only choice available with SM6 SM6 can be used with any of the DFT methods available in Jaguar or with the Hartree Fock approximation along with the MIDIX 6 31G 6 31 G or 6 31 G basis sets If you use the MIDIX basis set you must also select 6D for the Number of D functions in the Mole cule tab or set numd 6 in the gen section 3 10 Properties For each kind of wave function Jaguar can calculate various molecular properties The range of available properties depends on the wave function These calculations are normally performed using the converged SCF wave function By default none of the properties are computed but you can compute them by changing the settings in the Properties tab The exception is that SM6 solvation calculat
21. 96 129 density functional theory DFT 35 40 152 153 hybrid methoden 377 40 keywords eerte 169 176 210 Output TTOID aii tnter rnit 97 standard functionals 37 40 time dependent sees 35 density matrix convergence criterion essss 46 68 convergence criterion keyword 193 in DIIS error vector 96 129 keyword for output ess 208 density see electron density spin density derla proBram eee ete 234 Output from nre eiie 99 102 derlb program eerte 234 Output frOI eneie ti eterne 99 102 derivatives of basis functions 124 keyword for list in output 205 dftname values name strings for construction of 171 standard functional names 169 DFT see density functional theory dielectric constant keyWotds i iieiesete cierre brine tetris 187 Keywords for 187 setting in the Solvation tab 50 dielectric continuum method see pbf program DIIS convergence scheme 47 95 128 keyword for coefficient output 208 Eelere een 193 194 rond 96 dipole moment see multipole moments Direct Inversion in the Iterative Subspace method see DHS convergence scheme directory executable sissies 273 input installation local Mae
22. 97 prOperties icio Feet ditte tros 109 solvation calculations 102 output options 96 128 DTN ree etit 122 bond lengths and angles 122 connectivity table sess 123 detailed timing information 122 echo input file and parameter list 122 DER ee 124 125 206 207 Gaussian function list 123 geometry optimization details 123 memory disk and i o information 122 one electron Hamiltonian 123 Orbitals eines 125 128 207 210 overlap matze 123 per 1ter tioti eie rires 207 208 standard 121 124 204 205 UU GE 121 output summarizing 0 eee eee 87 92 output see output file output options standard output file output options per iteration output options orbitals babel overlap matrix in DIIS error vector 96 129 keyword for eigenvector and eigenvalue OULDUL 5st tee sed keyword for output of output Oopton essere smallest eigenvalue listed in output P parallel execution eese 301 jobs that can t be run oo eee 29 Jaguar 7 0 User Manual optimum processor number 302 selecting number of CPUS 24 parallel Jaguar module IBM installation
23. Contents 8 8 3 Basis Grid Dealiasing Function and Charge Usage for Individual Atoms 222 8 8 4 Defining Fragments in rr ert ior rt eb ie rd FU PIER VLA tlhe 227 8 9 The RGSS SOCOM a2anenaman etam ettet ota m ofthe efte aed 228 8 10 Th guess Section EE 229 8 11 The pointchi Section eue Mat M B Uu Re RH BER A HAB aa Mta se AEN 230 8 12 The E E TE 231 CFE EE 231 8 14 Theorbman Gechon sse nennen nennen 232 8 15 TINE E EE 233 8 16 Ihe ER EE 233 8 17 NBO SOU OMS noue cae osea en tuii said Marton uei o diis anaes 235 Chapter 9 Other Jaguar Files nauis stati rtt aired 237 9 1 The Basis Set File essence EES cessas 9 1 1 Basis Set Format 9 2 9 3 9 4 9 5 9 6 9 1 2 Effective Core Potential Format 9 1 3 Customizing BASIS Sels iei etes etie e UE Lie E DIA ERE IAS E LEE UR aa The Initial Guess Data File 242 The Dealiasing Function Pie 243 9 3 1 File Format and Description iiioisotena citi inest cud ick esed i eerte Id Eb ebrietas 244 9 3 2 Sample File Thi GEO EMG ooi ARI opui iiia as dan liec 248 9 4 1 File Eormat and UR le e EE 249 WME CUTOM File eee 252 Du 15cm 254 9 6 1 Describing Bonding Types in the Lewis Pie 255 9 6 2 Describing Hybridization Types in the Lewis File esses 257 9 6 3 Setting van der Waals Radii From Lewis File Data 258 9 6 4 Default Behavior for Setting Radii
24. Property Method alpha 3 pointfinite feld Finite field 0 0240 atomic units Job B3LYP 6 31G Single Point Energy Solvation Start Read Write Edit Reset Close Help Figure 3 8 The Properties tab showing controls for polarizabilities The options for the finite field method 17 can use a 3 point 5 point or 7 point finite difference method which uses the results from a number of SCF calculations one with no field and several with electric fields that are multiples of E and E in the x y and z directions E is 0 024 au by default You can use a different value by entering it in the Finite field text box 86 Keyword ipolar 1 for alpha or 2 for alpha and beta in the gen section 87 Keyword ipolar 5 in the gen section 88 Keyword ipolar 7 in the gen section Jaguar 7 0 User Manual Chapter 3 Options Both hyperpolarizability methods are run without using molecular symmetry Also for any polarizability calculation the energy convergence criterion which is set in the SCF tab is set by default to 1 0x10 For more information see Section 5 3 7 on page 109 and Section 8 5 14 on page 187 3 10 6 NMR Shielding Constants Gas phase NMR shielding constants are available for closed shell and unrestricted open shell wave functions 19 To calculate chemical shifts you should calculate NMR shielding constants for the reference molecule
25. normalization to that of the first component listed which is the x component Gaussian Functions Normalized coefficients S h t e y l p F atom 1 e n Z 0 T9 1 5484 671660 0 2 S 1 825 234946 0 3 S 1 188 046958 0 4 S 1 52 964500 O 5 S 1 16 897570 0 6 S8 1 5 799635 0 7 S 2 15 539616 O 8 S 2 3 599934 O 9 8S 2 1 013762 0 10 X 3 15 539616 Y 4 Z 5 0 11 X 3 3 599934 Y 4 Z 5 0 12 X 3 1 013762 Y 4 Z 5 0 831724 1 530816 2 477149 3 256281 2 792893 0 954938 0 617934 0 275721 0 814208 3 116944 2 401438 1 054360 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 1 000000 L 000000 0 831724 1 530816 2 477149 3 256281 2 792893 0 954938 0 617934 0 275721 814208 116944 116944 116944 401438 401438 401438 054360 054360 054360 kO p LP PD PO H C GA GA CD Jaguar 7 0 User Manual 119 Chapter 5 Output 120 0 13 S 6 0 270006 0 266956 1 000000 0 266956 O 14 X 7 0 270006 0 277432 1 000000 0 277432 Y 8 L 000000 0 277432 Z 9 L 000000 0 277432 0 15 Xx 10 0 800000 1 113825 1 000000 1 113825 YY 11 1 000000 1 113825 ZZ 12 1 000000 1 113825 XY 13 1 732051 1 929201 XZ 14 L 732051 1 929201 YZ 15 1 732051 1 929201 H1 1 S 16 18 731137 0 214935 1 000000 0 214935 H1 2 S 16 2 825394 0 364571 1 000000 0 364571 H1 3 S 16 0 640122 0 4
26. umotn Index of last alpha orbital for which to generate data relative to lowest unoccupied molecular orbital LUMO Ignored unless iorb1a is posi tive n can be any positive integer iorblb 1 Generate data for all beta orbitals 0 Do not generate any beta orbital data 20 Index of first beta orbital for which to generate data Ignored for restricted wave functions homotn Index of first beta orbital for which to generate data relative to highest occupied molecular orbital HOMO Ignored for restricted wave func tions n can be any positive integer Jaguar 7 0 User Manual 215 Chapter 8 The Jaguar Input File 216 Table 8 41 Keywords for generating plot data Continued Keyword Value Meaning lumotn Index of first beta orbital for which to generate data relative to lowest unoccupied molecular orbital LUMO Ignored for restricted wave functions n can be any positive integer iorb2b gt 0 Index of last beta orbital for which to generate data Ignored unless iorb1b is positive homoctn Index of last beta orbital for which to generate data relative to highest occupied molecular orbital HOMO Ignored unless iorb1b is positive n can be any positive integer lumo n Index of last beta orbital for which to generate data relative to lowest unoccupied molecular orbital LUMO Ignored unless iorb1b is posi tive n can be any positive integer plotres 2 9 Number of points per unit length
27. would describe a carbon atom 6 with one bond from carbon s Group 2 a double bond to either C or O and two bonds from carbon s Group 1 single bonds to H and would set such an atom s radius to 2 00 unless another matching description preceded that line The rightmost digit in the integer describing bonding type specifies the number of bonds formed by the atom which are not of any of the forms described in the groups for that atom s bonding type information A double or triple bond counts as one bond not two or three and lone pairs should not be included in the bond count The digits of the bonding type integer must describe all of an atom s bonding in order to match the atom information For example if the Lewis file described above contained no group for C C bonds in the bonding type information the integer 200 would only describe a carbon atom with one double bond to another C or O and no other bonds while the integer 202 would adequately describe a carbon with one double bond to another carbon and two single bonds to other carbon atoms The fourth integer in an atom type description which describes hybridization type or the elements and hybridization of the atoms to which an atom is bound works almost the same way as the integer describing bonding type As it does for bonding types the digit g places from the rightmost digit in the integer represents the gth group in the hybridization type infor mation for that ele
28. 178 suppression of use 11 relativistic effects sssssssssss 33 34 resonance in GVB calculations ssesseeeeeeeeeeeeeeeeee 44 in GVB LMP2 calculations 44 in LMP2 calceulatons 42 RESP file keyword sese 207 restarting calculations 136 137 GVB EE 217 initial GUESS ehe ned eb deter 132 restart file cierre 206 207 with improved euess eese 135 restricted configuration interaction see RCI calculations restricted open shell wave functions key WOT aine uim e 194 Jaguar 7 0 User Manual 343 Index 344 Maestro setting siisii 35 40 results summary of 87 92 nt E E 90 for each AtOM i eee 92 intermediate iisisti eraasi 91 RFO level shifting keyword for 181 Run Batch File panel sss 25 running jobs from Maestro 4 5 22 27 from the command line 266 268 initi p 24 27 on a remote bost eee eee eeeeeeee 266 troubleshooting sess 283 288 RvR information keywords for output of 205 EE DOSS eiecit cer terere tern 233 execution sequence S sample calculation sess 3 5 scaling frequencies sse 60 Ia M 191 Scam M 81 scanning Geometrie 80 84 SCF energy Output essen 95 SCF iterations Ido 207 maximum number of 45 134 S
29. 7 4 Pseudospectral Local MP2 Techniques Second order Mogller Plesset perturbation theory MP2 is perhaps the most widely used ab initio electron correlation methodology recovering a large fraction of the correlation energy at a relatively low computational cost The method greatly improves Hartree Fock treatments of properties such as transition states dispersion interactions hydrogen bonding and conforma tional energies However the scaling of conventional MP2 algorithms with system size is formally nN where N is the number of basis functions and n the number of occupied orbitals Jaguar 7 0 User Manual 149 Chapter 7 Theory 150 due to the necessity of carrying out a four index transformation from atomic basis functions to molecular orbitals In principle it is possible to reduce this scaling by using integral cutoffs as for Hartree Fock calculations However the reduction is noticeably less effective in MP2 particularly for the large correlation consistent basis sets that are required for accurate correla tion effects on observable quantities Thus MP2 techniques have traditionally been used primarily for small molecules Several years ago Pulay and coworkers 58 59 formulated a version of MP2 in which the occupied orbitals are first localized e g via Boys localization 61 and the virtual space correlating such orbitals are then truncated to a local space built from the atomic basis func tions on the local
30. All six integer values and a corresponding radius value must always be listed in an atom type description line and the atomic number must correspond to an actual element However any or all of the other five integer values can be set to 1 a wild card entry indicating that any value for that characteristic matches that atom type description To reset a default radius for hydrogen for instance you could put the following line before any other descriptions of hydrogen atoms t it ct f ci lt 1 1 10 H all 1 1 ignoring chemical environment and the van der Waals radius for all hydrogen atoms would be set to 1 10 To describe the hybridization of the atom itself the atom type description line s second integer should take on one of the values indicated in Table 9 3 The description of the atom s bonding type uses the groups listed in the bonding type informa tion described in Section 9 6 1 on page 255 unless it is 1 Any positive integer for bonding Jaguar 7 0 User Manual 259 Chapter 9 Other Jaguar Files 260 Table 9 3 Lewis file hybridization numbers and corresponding hybridization types Hybridization Corresponding Number Hybridization Type 1 s hybridization p hybridization d hybridization sp hybridization sp hybridization sp hybridization sp d hybridization VD 00 N QN t wow N sp d hybridization type describes the number of bonds the atom has in each of the bonding type groups for its element
31. For some systems the protonated and deprotonated structures adopt different conformations in the lowest energy state For such cases you should create Jaguar input files for both structures and use the deprot option of the jaguar pka command to specify the deprotonated struc ture Output files and results are in the same format as in the single initial geometry runs 13 4 7 Recalculating pK Values with New Parameters The utility script jaguar_pka can be used to recalculate pK values using parameters for a specified functional group The calculation takes the raw energies from a pK calculation and applies the correction factors for the specified functional group The syntax of the command is SSCHRODINGER utilities jaguar pka options jobname in The options are listed in Table 13 3 Table 13 3 Options for the jaguar pka script Option Description i Run in identification mode to identify the current functional group f name Specify the name of the functional group whose correction factors are to be used The name of the functional group must be specified in lower case and must be one of the functional group names listed in the Ga match xml file The standard names are the same as those in Table 13 1 except that they are always expressed in the singular not plural and given in lower case j filename Specify an alternate jres file Default is jobname jres m filename Specify an alternate pka match xml file Defa
32. see 115 Hartree Fock HF calculations DIIS error vector definition 129 keywords for SCF settings 193 196 output from standard 92 printing orbitals 123 208 Settings FOT uei eti etes 40 use for GVB initial guess 99 132 heat capacity calculations 62 63 115 191 Help panel 4 2 o sinisisi 283 Hessian e noseneeeneeoesosseeseeerreseeene 69 70 78 79 coordinates for refinement of 16 79 effect of quality on geometry convergence 69 78 input file section ssss 228 229 IRC calculations sonnooneoeenoneeeeaneaeeeee 85 184 keywords intime eine peers 180 181 leyel Shifting sec eet 181 refinement of initial 16 78 80 159 160 180 selecting initial 69 70 180 updating keyword for 180 heteroatom pairs OVNBcalceulatons local LMP2 calculations hfig prota cites ier output from sisisssrsisenste rsrsrs ureters hybrid methods DFT esses hybridization types describing in Lewis files 257 hydrogen bond energies batch script for 28 280 hyperpolarizability keywords cci reri eter thee 189 190 E EE 111 selecting options eect eee 55 57 in file see input file Index infrared ptensites 62 191 ini P 116 initial guess antiferromagnetic
33. 0 0 0 0 0 0 3 7005 0 0 0 2 T 20 0 3 7 3 2 5 0 0 0 2 1 0 00 3 02 1000 2 1 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 0 0 0 3 7 0 0 5 0 0 0 2 1 2 0 3 7 3 2 5 0 P H 2 d 0 03 02 1 0 0 0 2 1 2 00 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 9 4 The Grid File The grid input file grid file determines the grids used during the calculation Each grid type for example coarse or ultrafine is constructed from grids assigned to each atom in the molecule For any basis set for which the pseudospectral method is used the grid file must contain grids for each grid type used where each of these grid types in turn requires atomic grids for each element in the molecule Grids can be assigned to grid types in the input file using the gen section keywords gcoarse gmedium and so on Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files 9 4 1 File Format and Description The first line of a grid file contains a character string which includes the version number of Jaguar This string should be gridv followed immediately by four digits giving the version number times 100 Leading zeroes are added if necessary The next line should consist of an integer which gives the number of grid types described in the file For instance this number would be six if the grids specified were of the types coarse medium fine ultrafine eldens for electron density calculations and gradient By default Jaguar uses the
34. 1 28 1 34 1 48 1 44 1 41 1 40 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 1r 78 Pt 79 Au 80 Hg 81 TI 82 Pb 83 Bi 2 35 1 98 1 69 1 44 1 34 1 30 128 1 26 1 27 1 30 1 34 1 49 1 48 1 47 1 46 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 47 Keywords for listing basis grid dealiasing function and charge information for indi vidual atoms in an atomic section Keyword Value Description basis n no or none Use no basis functions on atom basis name Use basis functions from specified basis set on atom grid n no or none Do not include any grid points on atom only Include grid points on atom but no basis functions dealiasing functions or nuclear charge daf n no or none Do not include any dealiasing functions on atom only Include dealiasing functions on atom but no basis functions grid points or nuclear charge charge n no or none Treat atom as a counterpoise atom do not include nucleus or elec trons for atom only Include nuclear charge on atom but no basis functions grid points or dealiasing functions 8 8 4 Defining Fragments You can use the frag keyword in the atomic section to specify that all atoms with the same frag entry be treated in the same fragment You can then request that all the atoms in one frag ment be treated as dummy atoms or counterpoise atoms or used as the only atoms for which numerical frequencies will be calculated
35. 4 3 4 Refinement of the Initial Hessian The quality of the Hessian in the initial steps of a transition state optimization can have a marked effect on the speed of the job since the Hessian controls the direction the optimization takes on a potential energy surface in the search for an appropriate saddle point The QST 25 Keyword itrvec gt 0 in the gen section where itrvec is the relevant eigenvector number for the selected eigen vector 26 Keyword ifollow 1 in the gen section 27 Keyword ifollow 0 in the gen section Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans guided transition search method effectively refines the Hessian automatically in the first steps along the circular curve connecting the reactant transition state guess and product With the standard non QST guided optimization method if a coordinate with a negative force constant Hessian eigenvalue exists it is critical for this transition vector to be properly identi fied as efficiently as possible since it leads to the transition state Consequently for transition state searches with the standard optimizer when the initial Hessian chosen is a guess Hessian one not calculated numerically or read from a restart file it can be helpful to refine the Hessian during the calculation before using it to compute any new geometries Hessian refinement is especially likely to improve transition state optimizations that employ eigenvector follow
36. BLYP 6 31G 0 9945 BP86 6 31G 0 9914 B3LYP 6 31G 0 9614 B3P86 6 31G 0 9558 B3PW91 6 31G 0 9573 If the frequency job was not incorporated you can read the restart file into the Jaguar panel then import the vibrational data by choosing Import Vibrational Data from the Selection menu in the Project Table panel To view vibrational animations from calculations run with previous versions of Jaguar you can quickly generate the vib file using the Jaguar restart file from a frequency calculation using the following procedure 1 Read the restart file into the Jaguar panel The structure is displayed in the Workspace and an entry is created in the Project Table 2 Choose Initial Guess Only from the Jaguar submenu of the Applications menu 3 In the Properties tab select Vibrational frequencies in the table then select Use available Hessian in the Vibrational frequencies section 4 Run the job An alternative to steps 2 and 3 is to edit the input file and in the gen section change ifreq 1 to ifreq 1 and add igonly 1 The former setting means use available Hessian for calculating frequencies and the latter setting means skip the SCF Jaguar 7 0 User Manual Chapter 3 Options 62 BE Vibration vibration Entry 2 Frequency 2031 212 ay 571 192014 4 623 569683 765 362144 4 Animate Amplitude 1 000000 Slower Faster ECC mm Figure 3 1
37. C2 4 C2 1 7b Solving for the optimal GVB orbitals is therefore a matter of determining both the GVB natural orbitals and the GVB CI coefficients that minimize the energy of the GVB wave func tion This energy is given by the equation Jaguar 7 0 User Manual Chapter 7 Theory 2N ovp 2N d 2C hy ut gt ayyJ uv buv Kyy gvb 8 where u and v range over all GVB natural orbitals bonding and anti bonding and where these orbitals are expanded in terms of the basis functions as shown here N basis Y b3 Ciu The terms bn J uw Juv and Kuy are defined by N basis huy lal M Cine juhiy N basis E Se cac jy Sil N basis HU vv QJ uly bj Ciye jv ij N basis N basis d Ciyl jy Coy C G KT kl N basis Ru Ge uvjuv EK ayy 3 GE j N basis N basis S b3 CiyC jy 3 Cy Ci CK JT ij kl and the quantities a and Du obey the following rules uu 0 apy 0 byy E for u and v in the same pair u z v and 9 10a 10b 10c 11a 11b Jaguar 7 0 User Manual 145 Chapter 7 Theory 146 2 22 29 ayy 2C C Buy C C 11c for H and v in different pairs Examining the variation of the energy E with respect to the basis set coefficients c gives the equations for the Fock operator corresponding to each GVB natural orbital M 2 gt v v Fy Can 2 Cuvi t Buch 12 v Each orbital s Fock operator thus depends on the o
38. For medium and large molecules the additional overhead of the pseudospectral method in computing the transformation between physical and spectral space is vastly outweighed by the advantages of evaluating the integrals in physical space The matrix needed for the transforma tion from physical to spectral space 7 can be assembled before the SCF iterations by calcu lating the least squares operator Q which is given by the equation Q S R wR R w 1 where S is the analytic overlap matrix between the fitting functions and the basis set R is the matrix of fitting functions evaluated at the grid points and w is a diagonal matrix of grid weights The fitting functions used to construct the matrix R include both basis functions and dealiasing functions which are chosen in order to span the function space represented by the Jaguar 7 0 User Manual 141 Chapter 7 Theory 142 grid more completely than the basis functions alone The operator Q can be calculated for the relevant basis functions using several different sets of grid points where each set of points defines a grid type ranging from coarse to ultrafine In practice not all possible Qig elements are calculated for each basis function i and each grid point g because most basis functions drop off sharply enough that they have no significant value on some or most grid points These functions are classified as short range functions and are grouped together by atom while the
39. O 8 ui vj 1 3 5999336 0 1480263 0 2757209 O 9 a7 2 4 1 1 0137618 1 1307670 0 8142076 O 10 3 1 2 2 15 5396162 0 0708743 3 1169443 Jaguar 7 0 User Manual Chapter 5 Output O IL et0 2 2 O 12 10 1 2 2 O 13 1 1 5 0 14 1 2 6 0 15 1 0 3 9 H1 1 3 0 1 15 H1 2 0 1 15 H1 3 0 1 15 H1 4 0 1 16 H1 5 1 0 2 17 H2 1 3 0 1 20 H2 2 0 1 20 H2 3 0 1 20 H2 4 0 1 21 H2 5 0 2 22 CX C XR ah nd oo nd Fe De E bei 5999336 0137618 2700058 2700058 8000000 7311370 8253944 6401217 1612778 1000000 7311370 8253944 6401217 1612778 1000000 3397528 7271586 0000000 0000000 0000000 0334946 2347210 8137573 0000000 0000000 0334946 2347270 8137573 0000000 0000000 PP o or Foo OF Pr oo 4014375 0543604 2669562 27714320 138249 149354 645712 150514 6 057611 6457 VG GA H Oh PWN HIR H CO o CO ce ies a cO x eS E EE pex x1 Bai The second table an example of which follows below shows information for the Cartesian components of each shell For instance the entries X Y and Z for the tenth shell correspond to Px Py and p functions The normalization for each Cartesian component depends on the powers of x y and z in the polynomial for the component For 2 and higher the normaliza tion can be different for different components The rmfac values provide the ratio of the
40. The GVB treatment can also be applied to open shell cases or restricted to certain electron pairs These variations are described in Ref 22 which also provides much more detail about the GVB methods and equations The ability to restrict the use of GVB to particular electron pairs is an important strength of the method This feature allows computationally inexpensive correlation of critical regions in very large molecules 7 3 QGVB RCI Wave Functions The GVB RCI restricted configuration interaction wave function is the simplest multideter minantal reference wave function that properly dissociates to open shell fragments regardless of the spin multiplicity of the fragments A critical advantage of GVB RCI is that the GVB and RCI computations can be confined to a localized region of the molecule The GVB RCI method is therefore particularly useful for evaluating bond energies and bond formation and breaking as well as for studies of open shell radicals and other systems for which it is impor tant to avoid spin contamination problems The version of GVB RCI within Jaguar uses pseudospectral numerical methods and a novel internal contraction scheme in which a GVB PP wave function is used as a correlated mean field reference state 12 This implementation of GVB RCI can be used to generate highly accurate GVB RCI wave functions with energies within about 0 1 kcal mol of results from all analytical integral calculations 12 The internal contrac
41. The length units are defined by the iunit keyword The default given here is in points bohr xmaxadj 0 0 Amount to adjust the box boundary on the x axis Can be positive or negative xminadj 0 0 Amount to adjust the box boundary on the x axis Can be positive or negative xadj 0 0 Amount to adjust the x dimension of the box Half the adjustment is added to each boundary Can be positive or negative ymaxadj 0 0 Amount to adjust the box boundary on the y axis Can be positive or negative yminadj 0 0 Amount to adjust the box boundary on the y axis Can be positive or negative yadj 0 0 Amount to adjust the y dimension of the box Half the adjustment is added to each boundary Can be positive or negative zmaxadj 0 0 Amount to adjust the box boundary on the z axis Can be positive or negative zminadj 0 0 Amount to adjust the box boundary on the z axis Can be positive or negative zadj 0 0 Amount to adjust the z dimension of the box Half the adjustment is added to each boundary Can be positive or negative plotfmt vis or Set the format and file extension for plot files to vis the default Mae vis stro format plt or Set the format and file extension for plot files to p1t plt Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File The file name stem is jobname_density for a density plot jobname_spin for a spin density plot and jobname_potential for a potential plot Orbital plot information is written to sepa rate file
42. We use the cc pVTZ basis set of Dunning and coworkers in the present methodology The cc pVTZ basis set represents a mixed basis set where cc pVTZ is used for atoms involved in the deprotonation reaction while cc pVTZ covers the rest The residual errors in the DFT calculations appear to be relatively constant for a given functional group as the substituents are altered and hence can be largely removed by the empirical corrections 3 The solvation free energy of the protonated and deprotonated species must be computed We have chosen to do this using the gas phase geometries an approximation that we have tested and shown to be sufficient for the present purposes some of the errors induced are compensated by the empirical parameterization As we have discussed extensively in several publications empirical optimization of parameters is absolutely necessary to obtain accurate solvation free energies from SCRF calculation no matter what the level of electron correlation Continuum solvation methods do not rigorously treat effects at the dielectric boundary which therefore must be adjusted to fit experiment For neutral species we have optimized parameters both dielectric radii and surface tension terms by fitting to experimental gas to water solvation free energy data for small molecules Agreement to within a few tenths of a kcal mole can be obtained for most functional groups However parameterization of the model for ionic species
43. Winget P Truhlar D G Phys Chem Comm 2001 16 1 Li J Cramer C J Truhlar D G Theor Chem Acc 1998 99 192 Schafer A Huber C Ahlrichs R J Chem Phys 1994 100 5829 Hay P J Wadt W R J Chem Phys 1985 82 270 Hay P J Wadt W R J Chem Phys 1985 82 284 Hay P J Wadt W R J Chem Phys 1985 82 299 The LACV3P basis set is a triple zeta contraction of the LACVP basis set developed and tested at Schr dinger Inc Peterson K A J Chem Phys 2003 119 11099 Peterson K A Figgen D Goll E Stoll H Dolg M J Chem Phys 2003 119 11113 Metz B Stoll H Dolg M J Chem Phys 2000 113 2563 Cundari T R Stevens W J J Chem Phys 1993 98 5555 Hurley M Pacios L F Christiansen P A Ross R B Ermler W C J Chem Phys 1986 54 6840 Lajohn L Christiansen P A Ross R B Atashroo T Ermler W C J Chem Phys 1987 57 2812 Ross R B Powers J M Atashroo T Ermler W C Lajohn L Christiansen P A J Chem Phys 1990 93 6654 Ross R B Gayen S Ermler W C J Chem Phys 1994 100 8145 Ermler W C Ross R B Christiansen P A Int J Quantum Chem 1991 40 829 Nash C S Bursten B E Ermler W C J Chem Phys 1997 106 5133 Wildman S A DiLabio G A Christiansen P A J Chem Phys 1997 107 9975 Diffuse and polarization functions for Ga Rn taken from Dyall K G
44. a table lists the number of orbitals and of occupied orbitals in each shell having each irreducible representa tion for the appropriate point group Finally the orbital occupation for each shell is listed an occupation of 1 000 indicates a closed shell An example for a calculation of water using a 6 31G basis set follows start of program hfig initial wave function generated automatically from atomic wave functions Irreducible Total no No of occupied orbitals representation orbitals Shell 1 Shell 2 A1 12 3 A2 2 0 B1 4 1 B2 7 1 Orbital occupation shell 1 000 end of program hfig If the molecule contains a transition metal atom there may be several ways of occupying the d orbitals In this case hfig prints a list of the possible states and continues with the first of these It is possible however that a different initial occupation of the metal d orbitals would lead to a lower energy wave function To see whether this is the case you should run an SCF calculation for each of the possible degenerate states by selecting the state with the istate keyword An example for the FeH molecule follows Low energy states below 0 005000 hartree State Rel Energy MOs 9 10 11 12 313 metal d occupations 1 0 00000000 2 1 d 0 2 0 00000224 1 2 1 0 0 3 0 00062053 2 1 0 1 0 4 0 00062276 1 2 0 1 0 5 0 00071513 2 1 0 0 1 6 0 00071737 I 2 0 0 1 Jaguar 7 0 User Manual 93 Chapter 5 Output 94 WARNING
45. al Select Use pKa atoms from the Project Table When you select this option the Project Table opens if it is not already open If there is no pKa atom property in the Project Table you can add the property and a value for the entry in the Workspace by selecting Pick to Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module add atoms to Project Table then picking an atom in the Workspace structure To add val ues for other entries include them in the Workspace and pick the appropriate atom in each entry Make sure that this property is defined for each structure whose pK you want to calculate The pK atom should be the acidic hydrogen atom in an acid or the basic atom in a base You can use the conjugate acid or base as input but you should chose the hydrogen for a conjugate acid such as an ammonium ion or the heavy atom for the conjugate base such as a carboxylate You can submit a pK job for multiple molecules by choosing an option from the Use struc tures from option menu and including or selecting the target molecules or reading the input files For the last option the input files must already include the pK atom designation If you want to run pK calculations for each site in a single molecule that has multiple protona tion or deprotonation sites you can duplicate the entries select Duplicate from the Entry menu in the Project Table panel designate the pK atom for each entry and submit a job with the origi
46. button If you want to reopen it later you can do so by choosing Monitor Jobs from the Applica tions menu in the main window When the job finishes its output file is copied to the directory from which you started Maestro The output file ends with the extension out For instance if you entered the job name h2o the output file would be bio out If you want to exit Maestro choose Quit from the Maestro menu in the Maestro main window The Quit dialog box permits you to save a log file of the Maestro session For this exercise choose Quit do not save log file A warning dialog box is displayed which permits you to save the Maestro scratch project For this exercise choose Discard To check that the job ran correctly change to the directory where the output file was stored and enter the following command diff w jobname out SCHRODINGER jaguar vversion samples H20 out If there is no output from this command the job ran correctly If there is output examine the differences between the two files to see if the differences are significant If you are satisfied with the results of this sample run continue this chapter to learn more about using Maestro If you were unable to run the sample calculation see the troubleshooting suggestions in Chapter 11 Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro 2 2 The Jaguar Panel The Jaguar panel is the main interface between Maestro and Jaguar In this panel you c
47. calculates terms dependent on geometry e g nuclear repulsion energy onee Calculates one electron integrals and effective core potential ECP contribution to one electron Hamiltonian when relevant hfig Calculates Hartree Fock initial guess probe Ensures orthogonalization grid Generates grids rwr Generates Q operators gvbig Calculates GVB initial guess scf Performs self consistent field calculation rci Performs RCI calculation ch Evaluates electrostatic properties multipole moments electrostatic potential fit ting Mulliken populations Jaguar 7 0 User Manual 233 Chapter 8 The Jaguar Input File 234 Table 8 48 Individual programs included in Jaguar Continued Program Description lmp2dip Calculates dipole moments for LMP2 wave functions cpolar Finds polarizabilities and hyperpolarizabilities using coupled perturbed HF method polar Finds polarizabilities and hyperpolarizabilities using finite field method elden Calculates electron density on set of grid points local Performs localization of orbitals l1mp2 Performs local second order Meller Plesset perturbation theory calculation cis Performs CI singles calculation derla Calculate analytic one and two electron first derivatives derlb lmp2der Calculate analytic one and two electron first derivative terms for LMP2 wave lmp2gda functions lmp2gdb nude Calculates numerical second derivatives of energy as numerical derivatives of the analyt
48. entropy when degenerate sites are present This correction can be applied manually as needed after the 1 and 2 correction factors have been automatically applied by Jag uar see Section 13 2 2 on page 308 Jaguar 7 0 User Manual 319 320 Jaguar 7 0 User Manual Getting Help Schr dinger software is distributed with documentation in PDF format If the documentation is not installed in SCHRODINGER docs on a computer that you have access to you should install it or ask your system administrator to install it For help installing and setting up licenses for Schr dinger software and installing documenta tion see the Installation Guide For information on running jobs see the Job Control Guide Maestro has automatic context sensitive help Auto Help and Balloon Help or tooltips and an online help system To get help follow the steps below Check the Auto Help text box which is located at the foot of the main window If help is available for the task you are performing it is automatically displayed there Auto Help contains a single line of information For more detailed information use the online help If you want information about a GUI element such as a button or option there may be Balloon Help for the item Pause the cursor over the element If the Balloon Help does not appear check that Show Balloon Help is selected in the Help menu of the main win dow If there is Balloon Help for the element it appears w
49. esseri 188 output description sssssesesssseerereereeseeee 109 output option 122 tensors listed in output 109 units keyword eee 205 Murtagh Sargent method keyword 180 N Natural Bond Orbital NBO calculations sss 55 114 235 236 natural torsional angle constraints 72 83 162 neighbor Tanges eei reet trn es 244 nice option jaguar run command 267 NMR shielding constants key WOId eerte eterne 189 BEIER uiui geed EES 57 non local ensity approximation NLDA 153 n de protam E 234 number of iterations for geometry convergence MAXIMUM eeeeeeenneee hene 69 136 178 number of processors determining optimum e 302 SOLS CUTS sesinin ociscene insasi entest 267 numeric updating of Hessian keyword 180 numerical gradient of energy 67 keywords eire rares 178 180 numerical Hessian printing in freq output 205 numerical methods 141 143 cutoff file determination of 253 numerical second derivative of energy 58 key Words eterne memes 180 191 O OCBSE convergence scheme 47 Ones program ascia etre 299 output from sene 93 100 102 one electron Hamiltonian keyword for output Of 205 output Option iicet ette ECG Lee 123 one electron
50. jaguar Use structures from Workspace included entries d Molecule Theory scr Properties Solvation Output Properties select to edit options L Vibrational frequencies m eS Pa eS Surfaces MO density potential Atomic electrostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability L Surfaces Electron density Grid density 0 00 pts Spin density W Molecular orbitals Alpha Beta From HOMO 1 10 to LUMO s 0 Total number of orbitals 2 7 Electrostatic potential Box size adjustment 0 00 side From HOMO s 0 to LUMO s 0 Total number of orbitals 2 Job B3LYP 6 31G Single Point Energy Solvation Start Read Write Edit Reset The orbital selection controls depend on whether you have an initial guess or not If you do not have an initial guess you can select the orbitals to plot in a range relative to the HOMO and LUMO If you do have an initial guess a list is displayed with the orbital index energy and occupation You can select a range of orbitals from this list with the SHIFT key If the wave function is spin unrestricted you can choose alpha and beta orbitals independently When the job to generate the data finishes the surfaces are imported into Maestro and the first
51. keywords 210 212 selecting DEL udo rhet 36 shells for in grid file 249 250 specified in cutoff file 253 grids pseudospectral accuracy level sess 45 194 basis set availability sss 31 keywords eee 195 211 212 GVB calculations 43 44 143 147 from HF converged wavefunction 132 198 generating GAUSSIAN input for 140 GVB data out 208 HF initial euess eee 132 input HF wave function 198 keywords 165 166 output TOM iid 0 Greiner 98 99 pair selection Ups 136 printing orbitals oes 126 209 SC TE 217 troubleshooting eee 288 GVB pairs definition eto teintes 144 for GAUSSIAN input seen 140 heteroatom input file section for 217 218 output Information 98 99 Selection tIps o etre 136 setting from Lewis dot structure 166 Jaguar 7 0 User Manual troubleshooting eee 288 gvbig prOgraim oeeo esos 98 233 GVB LMP 2 calculations sess 44 GVB RCI calculations 147 149 H Hamiltonians information in output 95 98 99 user input of 231 232 harmonic constraints eeessees 72 162 harmonic frequencies
52. of the second natural orbital in the calculation If a GVB calculation is performed from a Hartree Fock converged wave function the program scf runs twice once to obtain the HF converged wave function and once to perform the final GVB calculation The SCF output from the first sc run will look like the SCF output from a standard HF calculation the output from the second run will have the format described above for a GVB calculation from an HF initial guess 5 3 4 Geometry or Transition State Optimization The output format description for optimizations in this subsection applies to calculations of either minimum energy structures or transition states Although the Hessians used during these calculations are different the Jaguar programs run are the same and the output format is very similar Exceptions are described below If you calculate an optimized molecular structure a transition state or forces any SCF calcula tions during the run use the RMS density change convergence criterion described in Section 3 8 on page 45 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed for several more iterations than single point energy calculations If you select forces only for the Optimize geometry setting the programs derla rwr and derlb will run after scf does The forces felt by each atom in the unoptimized geometry will be output from der1b in a table listing each atom and the components of
53. quality initial guess using ligand field theory as described in Ref 21 Not available for GVB calculations For a system that contains transition metal atoms construct a high quality initial guess using ligand field theory including d d repulsion as described in Ref 21 Not available for GVB calculations ihfgvb 0 Jaguar 7 0 User Manual a Read in GVB initial guess from guess section if iguess 1 and do not run hfig or gvbig programs or b Compute it from HF initial guess whose origin is determined by iguess if iguess 1 Converge HF wave function where the initial guess is determined by iguess and use converged HF wave function as input to program gvbig to get GVB initial guess Calculate a GVB initial guess from HF initial guess whose origin is determined by setting iguess Chapter 8 The Jaguar Input File Table 8 29 Initial guess keywords Continued Keyword Value Description ihamtyp 0 Construct Hamiltonian using standard core open and GVB orbitals 2 Make highest two orbitals in initial guess an open shell singlet pair ROHF only 3 Input Hamiltonian in ham section ihamtyp 3 by default if a non empty ham section exists ioss 0 Use the default open shell guess 1 Set up an open shell singlet initial guess by mixing the LUMO into the HOMO and set isymm 0 and iuhf 1 See text istate 0 Use the default state selection when there are degenerate states in tran sition metal systems Same as settin
54. s bonding types are about to be described in the same format After all desired bonding types are described for all appropriate elements the bonding type information should end with a blank line Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files 9 6 2 Describing Hybridization Types in the Lewis File The hybridization type information in the Lewis file includes up to five groups for each element described where each group indicates a set of elements and hybridizations for those elements The hybridization applies to the atom to which the original element is bonded The information for hydrogen s first group for instance could list C atomic number 6 with sp hybridization allowing a later line in the Lewis file to set a particular radius for hydrogen atoms bonded to sp carbons The format of the hybridization type information is very similar to that of the bonding type information The first line of this information for HF GVB or DFT calculations should begin HYBRIDIZATION TYPE 01 and the rest of the hybridization type information should not contain any blank lines except the last line which signals the end of hybridization type information Hybridization type information should be listed for each relevant element in turn The informa tion for the first atom should follow immediately after the HYBRIDIZATION TYPE 01 label The first character of the information for that atom should begin with the atom s atomic number
55. surface is displayed For geometry scans the surfaces are associated with the correct point in the scan If your molecule is not already an entry in the Project Table the surfaces are not auto matically incorporated To display the surfaces create an entry in the Project Table for the Jaguar 7 0 User Manual Close Help Figure 3 11 The Properties tab showing controls for surfaces Chapter 3 Options chosen molecule and select it then choose Import from the Surfaces submenu of the Display menu The Import Surface Volume Data dialog box is displayed and you can navigate to the vis files for the surfaces and import them Then choose Surface Table from the Surfaces submenu of the Display menu to open the Surface Table panel You can view multiple surfaces for the same molecule but they are superimposed If you want to view multiple surfaces e g plots for several orbitals from the same molecule side by side you must duplicate the Project Table entry for the molecule as many times as you have orbitals to view then display a separate orbital surface for each entry In addition to displaying isosurfaces for the data generated by Jaguar you can display the value of the property for which you generated the data as a color map on another surface that is generated by Maestro For example you can display the value of the electrostatic potential on the van der Waals surface generated by Maestro To do this select the surf
56. use Z matrix form for your geometry input and set all rele vant bonds equal to the same variable See Section 2 4 4 on page 11 and Section 2 4 6 on page 14 for more information 3 7 QGVB LMP2 Settings Jaguar s pseudospectral GVB LMP2 module allows this multireference perturbation method to be applied to medium and large molecules with reasonable CPU memory and disk use The method has been shown to give highly accurate conformational energies 20 For GVB LMP2 calculations Jaguar first performs an SCF calculation of the reference GVB wave function using the GVB pairs specified in the input Next the program applies an LMP2 perturbative correction to the energy The LMP2 calculation is performed on the entire system even if only part of the system was treated at the GVB level To set up a GVB LMP2 calculation choose GVB LMP2 from the Level of theory option menu in the Theory tab The calculation is performed on all atom pairs If you want to restrict the atom pairs used you must edit the input file and add the appropriate keywords You can control the localization of the orbitals and the delocalization due to resonance just as for Hartree Fock based LMP2 calculations see Section 3 5 on page 40 We advise using GVB LMP2 primarily for single point energy calculations since Jaguar cannot compute GVB LMP2 atomic charges or analytic gradients For best results with GVB LMP2 first run your calculations with the 6 31G basis set then chang
57. where Hessian elements for other atoms are zero The default frag value for each atom is 0 meaning it is not considered part of any fragment To assign a group of atoms to the same fragment in the frag column of the atomic section enter the same value for each atom To treat all atoms in a fragment as counterpoise atoms set icpfrag fragno in the gen section of the input file where fragno is the integer fragment label from the frag column of the atomic section To treat them all as dummy atoms make the keyword setting idelfrag fragno in the gen section To compute partial frequencies for a particular fragment make the setting freqfrag fragno in the gen section of a frequency input file One further use of fragments is for antiferromagnetic systems for which standard transition metal initial guesses do not work For an antiferromagnetic system containing two metal atoms that are not bonded you can use a 2spin column to set up the initial guess When the metals are within bonding distance or when there are more than two metals you should assign the metal atoms to separate fragments using the frag column of the atomic section Finally add formal and 2spin values in the atomic section Jaguar 7 0 User Manual 227 Chapter 8 The Jaguar Input File 228 8 9 The hess Section If an input file has a non empty hess section the keyword inhess in the gen section is set to 2 automatically and a Hessian is read in from the hess sect
58. 000000 0 137251 H 1 124354 0 811712 0 387157 H 1 124358 0 811709 0 387157 C 0 709471 0 000000 0 018344 H 1 090939 0 000000 1 056719 H 1 113065 0 885399 0 490174 H 1 113060 0 885402 0 490171 amp After the gas phase SCF calculation is complete molecular properties are computed and printed out from the program ch For SM6 calculations these include in addition to any other molecular properties that you specify atomic L wdin populations atomic redistributed L wdin populations if diffuse basis functions are used and CMA partial atomic charges This output is given here start of program ch Atomic charges from Lowdin population analysis Atom N1 H2 H3 C4 H5 Charge 56393 25338 25338 37504 12513 Jaguar 7 0 User Manual Chapter 5 Output Atom H6 H7 Charge 15354 15354 sum of atomic charges 000000 Atomic charges from CM4 Atom N1 H2 Charge 71682 28490 Atom H6 H7 Charge 06138 06138 sum of atomic charges 000000 end of program ch H3 28490 c4 01083 H5 03508 Once all of the gas phase molecular properties have been computed the solution phase SCRF calculation is performed Output from this part of the calculation is printed out from the program scf This output is given here start of program scf Energy components in hartrees A H D Gone a M Nucl Tota El Ki Ex Elec ear repulsion l one electron terms ectron nuclear NEED i
59. 3 parameter hybrid you must list a purely local correlation func tional which will be used to adjust the local correlation contribution For Becke 3 parameter hybrids that do not include the Lee Yang Parr functional the coefficients of the exact HF exchange and of the local exchange non local exchange local correlation and non local correlation functionals are 0 2 0 8 0 72 1 0 and 0 81 respectively If the Lee Yang Parr func tional is used in a Becke 3 parameter hybrid its coefficient is 0 81 and the coefficient of the local correlation functional used is 0 19 If idft 1 the values of the keywords xhf xexl1 xexl9 and xexnln determine the contribu tions of the exact exchange and the exchange functionals while the keywords xcorln and xcornlz control the contributions of the correlation functionals as listed in Table 8 15 For example with idft 1 xhf 0 332 xexl1 0 575 and xcorl1 0 575 and with all other xex and xcor keywords set to zero the exchange is treated with a combination of the exact exchange and the Slater local functional while the correlation functional is pure VWN Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File If you want to evaluate the energy of the final post SCF wave function using a particular func tional or combination of functionals you should use the keyword jdft This keyword can take on the same values as idft and the meanings for each value are the same as those described above
60. 3b for the appropriate choices of i j k and must be subtracted from the pseudospectral J and K elements as well This combined pseudospectral analytic approach allows Jaguar to take advantage of the strengths of both methods since it can largely maintain the pseudospectral method speedups for a particular grid and can also use a coarser grid than a purely numerical calculation would allow 7 2 Pseudospectral Implementation of the GVB Method The pseudospectral method has also been extended to electron correlation methods particu larly for Generalized Valence Bond GVB 22 calculations Highly refined GVB initial guess 14 and convergence 11 algorithms have been automated within Jaguar allowing the scaling advantages of the pseudospectral method to be maintained for GVB calculations The method yields very accurate excitation energies rotational barriers and bond energies for many mole cules and GVB calculations with Jaguar are typically 10 to 100 times more efficient than the best conventional GVB programs even for molecules as small as ten atoms 6 In the GVB approach each bond or other electron pair is described by two non orthogonal orbitals whose contributions to the bond description are obtained variationally The bond description can thus change smoothly from a description with two atomic like orbitals at large bond distances to a description with bond like orbitals at short distances This improvement over Hartree Fock
61. C J Truhlar D G J Comp Aided Mol Design 1992 6 629 Marten B Kim K Cortis C Friesner R A Murphy R B Ringnalda M N Sitkoff D Honig B New Model for Calculation of Solvation Free Energies Correc tion of Self Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen Bonding Effects J Phys Chem 1996 100 11775 Kelly C P Cramer C J Truhlar D G SM6 A Density Functional Theory Continuum Solvation Model for Neutrals Ions and Ion Water Clusters J Chem Theory Comput 2005 1 1133 Hoijtink G J Boer E D Meij P H v D Weijland W P Recl Trav Chim Pays Bas 1956 75 487 Tucker S C Truhlar D G Chem Phys Lett 1989 157 164 Still W C Tempczyk A Hawley R C Hendrickson T J Am Chem Soc 1990 112 6127 Zhu T Li J Hawkins G D Cramer C J Truhlar D G Density Functional Solva tion Model Based on CM2 Atomic Charges J Chem Phys 1998 109 9117 Cramer C J Truhlar D G In Reviews in Computational Chemistry Boyd D B Lipkowitz K B Eds VCH Publishers New York 1995 Vol 6 pp 1 Cramer C J Truhlar D G Chem Rev 1999 99 2161 Liotard D A Hawkins G D Lynch G C Cramer C J Truhlar D G Improved Methods for Semiempirical Solvation Models J Comput Chem 1995 16 422 L wdin P O J Chem Phys 1950 18 365 Baker J Theor Chim Acta 1985 68 221 Jaguar 7 0
62. DFT techniques To use jaguar batch you need a batch input file whose name should end in bat and at least one input file The input files can provide structures in either Maestro or Jaguar format or can provide templates for running the calculations The batch input file tells jaguar batch how to create a Jaguar input file or modify a template input file for each Jaguar job These modifications can include changes to particular bond lengths and angles of the structure changes in the wave function or job type such as changing an HF geometry optimization input file to a DFT single point energy calculation input file changes in the files or directories used for jobs and virtually all other settings made in input files One batch input file can be used to request several different input files either from one template input file or from several different templates The jaguar batch command then generates the input files and runs the corre sponding jobs either consecutively if only one host has been specified or by distributing the jobs over the specified hosts 10 2 1 Batch Input File Format Batch input files can include directives job specifications UNIX commands and comments Lines that contain comments must begin with a symbol and lines that contain Unix commands must begin with a symbol Blank lines can also be used in the batch script and are ignored The available directives are summarized in Table 10 4 The directives apply
63. E needgwd newcon nhesref nogas nogdiis incu M nosuper noupdat nrestart Jaguar 7 0 User Manual 349 Keyword Index 350 X MA m 216 xcorl1 xcorl4 174 175 xcornll1 xcornl9 174 175 s Cr A i DE 174 175 jo 174 175 Sexvnll sexvnll5 175 xexnl1 xexnlO9 ssseesseesseee 174 MMP iussus 174 175 xmaxad tct tei treibt 216 xminadj i4 tienes eto eroe edid 216 Y Z EL E 216 KO RE 216 Znad jian rete 216 ZInpmelin o eo mre sereno 213 Jaguar 7 0 User Manual 120 West 45th Street 101 SW Main Street 3655 Nobel Drive Dynamostrafe 13 QuatroHouse Frimley Road 29th Floor Suite 1300 Suite 430 68165 Mannheim Camberley GU16 7ER New York NY 10036 Portland OR 97204 San Diego CA 92122 Germany United Kingdom SCHRODINGER
64. Energy Decomposition Analysis calculations from Jaguar however For more details on NBO input and output see the NBO 5 0 Manual or visit the NBO web site http www chem wisc edu nbo5 3 10 5 Polarizability and Hyperpolarizability You can calculate polarizabilities and first and second hyperpolarizabilities by selecting Polar izability Hyperpolarizability in the Properties table and making the appropriate choice from the Property Method option menu The calculations can be done analytically or with a finite field The analytic method 18 calculates the polarizability and hyperpolarizabilities by solving the coupled perturbed Hartree Fock CPHF equations 9 In general this method is superior to the finite field method but the CPHF option can be used only with closed shell and unrestricted open shell wave functions 84 Empty nbo section in the input file 85 Keyword ipolar 1 and 2 in the gen section Jaguar 7 0 User Manual 55 Chapter 3 Options 56 Jaguar jaguar la Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Properties select to edit options L Vibrational frequencies Surfaces MO density potential Atomic electrostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability 4 Polarizability Hyperpolarizability
65. Extra Output The options available in the Output tab of the Jaguar panel under Extra detail to be written to output file are described in this section These options are presented as a list from which you can select multiple items with the SHIFT and CTRL keys The output generated from these options appears in the output file for the job If you make a non default setting the output from the program pre prints the non default options chosen This output appears above the molecular geometry output from pre and gives the non default values of the keywords referred to in footnotes throughout this section Jaguar jaguar DIE Use structures from Workspace included entries Molecule Theory scr Optimization Scan Properties Solvation Output Write input files in the selected formats Extra detail to be written to output file Gaussian input file gau GAMESS input file gamess Spartan archive file arc XYZ file xyz Molden orbitals file molf Echo input file and parameter list Memory disk and I O information Detailed timing information RN 1 KI m Orbital Coefficients Calculation stage After HF initial guess After SCF After final localization Each iteration in CO space Each iteration in AO space Orbitals Occupied Format Large values f5 2 labels list Job HF 6 31G Relaxed Coordinate Scan Start Read Write Edit Re
66. GUI you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the GUI or if you want to edit keywords directly by using the Edit Job window described in Section 2 3 on page 8 3 1 Molecule Settings The top part of the Molecule tab provides controls for the molecular charge the spin multi plicity and the application of molecular symmetry Setting charge and spin multiplicity was discussed in Section 2 6 on page 18 Briefly you can enter the charge and spin multiplicity in text boxes or you can use values that are listed in the Project Table If you choose the latter you can create the corresponding properties and enter values for them if they don t exist By default Jaguar takes advantage of molecular symmetry in order to obtain CPU savings Both Abelian and non Abelian point groups are recognized You can select whether to use the full symmetry Abelian symmetry D2h and subgroups or turn the use of symmetry off in Jaguar 7 0 User Manual 29 Chapter 3 Options 30 the Symmetry option menu For information on how to make sure the symmetry of your input structure is treated as you expect see Section 2 7 2 on page 19 For some calculations including GVB LMP2 GVB LMP2 calculations and calculations of IR intensities or hyperpolarizabilities symmetry is not implemented and is disabled automatically during the job 3 2 Basis Sets In the lower part of
67. GUI equivalent is described in Section 3 5 on page 40 is not keyword based The section should contain a line for each atom pair describing atoms to be treated at the LMP2 level Each line describing an LMP2 pair should begin with two atom numbers or labels which specify the two atoms in the pair Pairs can be listed in any order The following Imp2 section requests treatment of atoms 6 9 and 10 in the zmat section at the LMP level and all other atoms at the Hartree Fock level Atom 9 is bonded to atoms 6 and 10 amp lmp2 6 9 9 10 amp You can also use the Imp2 section of the Jaguar input file to list particular LMP2 pairs and request that they be delocalized over listed atoms With LMP2 delocalization the space of correlating virtual orbitals for an LMP2 occupied orbital is extended to include orbitals on nearby atoms To delocalize a bond pair on two particular atoms over a space including orbitals on a set of other atoms add a line to the Imp2 section listing the atom labels or numbers of the two atoms upon which the bond pair is located by default followed by the atom numbers or labels of the atoms over which the pair is to be delocalized Next set the keyword idelocv in the gen section to 1 to treat all LMP2 pairs in the system or 2 to perform a local local MP2 calculation with only the pairs listed in the Imp2 section treated at the LMP2 level For example the following gen and Imp2 sections request a local local MP2 calc
68. If the esp column entry for a TI dummy atom is y or yes it will be included in the charge fit Several warnings apply to the use of the esp column First the esp settings must not be incon sistent with the symmetry used for the rest of the job Second you should be careful not to overconstrain the charge fitting job Third if you are including any dummy atoms in the charge fitting it may be advisable to perform the charge fitting in a separate job based on the restart file for which the charge fitting grid has been altered to include points around the dummy atoms by including a grid column in the atomic section with y or yes entries for the dummy atoms as described below The van der Waals surface used for charge fitting is constructed using DREIDING 72 van der Waals radii for hydrogen and for carbon through argon and universal force field 69 van der Waals radii for all other elements These radii are listed in Table 8 43 and can be changed using the vdw keyword Jaguar 7 0 User Manual 221 The Jaguar Input File Chapter 8 spioM o oS1eqo pue zep pris oy 10j 3 negop ensn ou popnypour ore wow Jey 10 sooned posaeuo Jo uonoung Surseieop PUS 201 jeu sojeorpur sayy VISAI ur Ieadde Ae yey gata A ou se qons IM JO pioA 19470 Aue jeu 30u OSTY 4 58 ALL 995 oSeuo pepmue uuingoo 201 ur 0 jo Aue ue Sursn Aq poyeorpur are suroje esrodiojunoo uonoos 3ruroge 201 ut ndur osrodio
69. J and K are kept in core rather than on disk if basis functions x Hamiltonians ndisk Hamiltonians 1 for closed shell and 2 for open shell mxpr 100 Pairs of dealiasing functions are organized so that each group s pairs have the same angular momentum values e g a group with pairs with an s and a p function The number of pairs in each group evaluated at the same time by subroutine novoro is restricted so that it is lt mxpr zmpmem 1 0 For LMP2 single point and gradient code maximum total size allowed for arrays holding partially transformed integrals on grid is 60 MB x zmpmem Note If you set iqgrad you must set iqufine to the same value Table 8 40 Keywords to determine when to compute the full least squares fitting matrix Q Keyword Value Description iqcoarse 0 For coarse grid compute Q on the fly in the program scf 1 For coarse grid compute Q in the program rwr and store on disk for later use Jaguar 7 0 User Manual 213 Chapter 8 The Jaguar Input File 214 Table 8 40 Keywords to determine when to compute the full least squares fitting matrix Q Keyword Value Description iqmedium 0 For medium grid compute Q on the fly in the program scf 1 For medium grid compute Q in the program rwr and store on disk for later use iqfine 0 For fine grid compute Q on the fly in the program scf 1 For fine grid compute Q in the program rwr and store on disk for later use iqufine 0 For ultra
70. LMP2 is on unless Imp2 section exists if LMP2 is on and Imp2 section exists set atom pairs in Imp2 section 1 Treat only heteroatom pairs atoms in bonds with atoms of other ele ments except C atoms bonded only to C and or H and any pairs set in Imp2 section at LMP2 level other atoms at HF level ireson 0 Do not delocalize LMP2 pairs over other atoms 1 Calculate Lewis dot structure of molecule by setting lewdot 1 then delocalize LMP2 pairs on any bond in an aromatic ring of lt 7 atoms over neighboring atoms in the aromatic ring 2 Calculate Lewis dot structure of molecule by setting lewdot 1 then delocalize LMP2 pairs on any bond in an aromatic ring of lt 7 atoms over all atoms in the aromatic ring idelocv 0 Do not delocalize any pairs listed in Imp2 section default for all calcula tions except those with iqst gt 0 and or ireson gt 0 1 Treat all LMP2 pairs but delocalize any pairs in Imp2 section as indi cated there or default for QST guided transition state searches delocal ize any pairs on atoms with breaking or forming bonds 2 Perform a local local MP2 calculation treating only pairs listed in the Imp2 section at the LMP2 level and also delocalize any pairs in Imp2 section as indicated there loclmp2c 0 Do not localize core orbitals for LMP2 calculation 1 Perform Boys localization on core orbitals for LMP2 calculation 2 Perform Pipek Mezey localization on core orbitals for LMP2 calculation maximizing Mulliken atom
71. Manual 313 Chapter 13 The pK Prediction Module 314 amp zmat C1 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H1 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat H1 amp amp zmat C1 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H1 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat 4 amp When the pK job is run Jaguar checks that the functional group containing the designated pK atom has correction parameters available If it does not the job fails immediately and an error message explaining the problem is printed to jobname out If you want to calculate a raw pK value using the Jaguar methods but without correction factors you can set ipkaraw 1 in the gen section of the input file You might want to do this when developing your own correction factors see Section 13 5 on page 318 13 4 4 Running pK Calculations from the Command Line To submit a pK job for a single molecule using the command line use the following command jaguar pka PROCS nproc jobname acid and base files If the acid and base conformations are similar you need only specify one input file jobname in which can contain a structure for an acid or a bas
72. PROCS Use nprocs processors for a parallel job Run a serial job nprocs Replaces p NICE Run Jaguar executables with nice 19 Jaguar executables are run without nice Replaces n FORCE Force the scratch directory to be over Abort the job if a scratch directory written if it exists Replaces F named for the job already exists Write time stamps to the log file after Write time stamps to the log file at the each executable has run start and the end of a job DEBUG Print debug information in the terminal Do not print debug information window This information is useful if you need to contact technical support where your input file is named jobname in and hostname is one of the hosts in the file schrodinger hosts For instance if you were logged into a machine named alpha and wanted to run a job named ch4 on a machine named beta you would enter jaguar run HOST beta ch4 To run a Jaguar job on the machine hostname with a particular non default set of executables you can use the command jaguar run HOST hostname VER version jobname Jaguar 7 0 User Manual Chapter 10 Running Jobs 268 where version is any string that appears in one of the executable directories listed for that host by the command jaguar LIST HOST hostname The string must be unique to ensure that the desired executables are selected The jaguar run command has several other command line options as shown in Table 10 2 For example ja
73. REMOTE_JAGUAR_EXEC SCHRODINGER jaguar vjversion bin Linux arch T REMOTE_MMSHARE_EXEC SCHRODINGER mmshare vmversion bin Linux arch LD_LIBRARY_PATH SCHRODINGER mmshare vmversion lib Linux arch SCHRODINGER jaguar vjversion lib Linux arch where jversion is the 5 digit Jaguar version number mversion is the 5 digit mmshare version number and arch is either x86 or ia64 You must also ensure that the mpirun script is in your PATH If the installation directory is different on different hosts for example if you have a Linux cluster on which SCHRODINGER opt schrodinger and a desktop computer on which SCHRODINGER software schrodinger you must make the SCHRODINGER setting depen dent upon the value of HOSTNAME in your shell startup scripts so that the correct installation directory is located on each host Jaguar 7 0 User Manual Chapter 12 Parallel Jaguar 12 1 2 4 Selecting Nodes for a Job Job queuing software such as SGE or PBS is often used on computer clusters to assign nodes and manage the load If you are not using job queuing software you can select the nodes that a job will run on in the following ways Select the nodes using the HOST option of the jaguar run command The list of nodes must be enclosed in quotes For example SSCHRODINGER jaguar run HOST homer bart PROCS 2 ethane in Create a local machines LINU
74. Rr RIP aaea Ei 54 3 10 3 Multipole Klee 22 21 2 5 e ant uide ttesio en nitet iie EES 55 3 10 4 Natural Bond Orbital NBO AnalySiS AA 55 3 10 5 Polarizability and Hyperpolarizability eee 55 3 10 6 NMR Shielding Constants uec irri rea e iter eiie ager eed th ee 57 3 10 7 Molecular Properties from SM6 CGalculattons AAA 57 Jaguar 7 0 User Manual Contents 3 11 Frequencies and Related Properties AAA 58 Em IU P ee cenieee nett teenie esas 58 3 11 2 Atomic EE 59 3 1 1 3 SCaling OF FREQUENCIES ossi ioo DAR PUERO ERO DURO MM AMBIEN U DES 60 311 4 lee 60 3 11 5 Infrared Intensitles seiten oiana srini eene eic tree aded bul i die 62 3 11 6 Thermochemical Properties 2 en endete tenerte noc dicta pne iaia 62 KEEPS 63 Chapter 4 Optimizations and Scans 67 4 1 Geometry Optimization The Basics 67 4 1 1 SGF and Geometry e ee ead vie EA AERE a ARE 68 41 2 The Initial Hessian m 69 een 70 4 2 Constraining Coordinates sse 70 4 2 1 Freezing Specific Coordinates iere eie rtr e Ft e reet ve de os aea 71 42 2 Applying Manone CODstFall ite usitas aree ERES FAR ATE ati EE ERA ERA URS T2 4 2 3 Applying Constraints by Using Variables A 73 4 2 4 Applying Dynamic Gonstraints 2 2 ccn recette med Edel cet tede 74 4 3 Transition State Optimizations sss 74 4 3 1 Transition State Search Method eee 7
75. S for s X for p etc and calculated population If you calculate them by bond the populations by atom and basis function are given as well An example for water in a 6 31G basis set follows Mulliken Bond Populations first nearest neighbor Atoml Atom2 Pop Atoml Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop H1 O 0 314 H2 0 0 314 Mulliken Bond Populations second nearest neighbor Atom1 Atom2 Pop Atoml Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop H2 H1 0 025 Mulliken population for basis functions atom func type population 0 1 S 1 9954 0 2 S 0 8942 O 3 X 0 8034 O 4 Y 0 9514 O 5 Z 1 1426 O 6 S 0 8865 O 7 X 0 4669 O 8 Y 0 6649 O 9 Z 0 8332 O 10 XX 0 0085 0 11 YY 0 0024 Oo 12 ZZ 0 0052 O 13 XY 0 0142 Oo 14 XZ 0 0000 O 15 YZ 0 0021 H1 16 S 0 4950 Jaguar 7 0 User Manual 113 Chapter 5 Output 114 H1 17 S 0 1263 Hl 18 X 0 0185 Hl 19 Y 0 0138 H1 20 Z 0 0111 H2 21 S 0 4950 H2 22 S 0 1263 H2 23 X 0 0185 H2 24 Y 0 0138 H2 25 Z 0 0111 Atomic charges from Mulliken population analysis Atom 0 H1 H2 Charge 0 67059 0 33530 0 33530 sum of atomic charges 0 000000 You may find it helpful to select the Gaussian function list basis set setting in the Output tab if you want to have more information about the basis functions More information on this output option is given in Section 5 4 on page 121 If both Mulliken populations and multipole moments are calculated the multipo
76. SCF iteration ip102 At end of job ip103 In atomic orbital space each SCF iteration ip104 In atomic orbital space after SCF Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 35 Keywords that specify when to print orbitals Continued Keyword Prints Orbitals ip105 For HF initial guess ip106 For GVB initial guess ip107 After Boys or Pipek localization Table 8 36 explains the possible values for the orbital output options aside from 1 the default which turns off printing The variable n in the table can be either 0 5 or 10 If it is 0 all occu pied orbitals including GVB natural orbitals are printed If n is 5 all occupied orbitals and ipvirt virtual orbitals are printed or all virtuals if ipvirt 1 Setting n to 10 causes only the GVB non orthogonal orbitals to be printed Table 8 36 Dependence of the format and type of orbital output on the value of ipx Value of ipx 24n 34n 44n Bin Bin Format f5 2 f10 5 f19 15 f8 5 e15 6 Atom basis function type Y Y N N N shown Orbital occupation indicated Y N Y Y N Coefficients printed large all all all all Form shown list table list list table a The value of n determines which orbitals e g occupied are printed x determines the stage at which orbitals are printed see Table 8 35 For example ip106 10 means that all orbitals are to be printed in Fortran f8 5 format after the GVB initial guess is created The options ip105 12 are not valid
77. The following lines should describe up to five hybridization groups for that atom Each group must begin with the word Group with no leading spaces The group is a list of bonded atoms for all relevant hybridization types of those bonded atoms for instance Group 2 for hydrogen could describe hydrogens bonded to sp carbons by listing carbon s atomic number under an sp hybridization label Because there is no default number of hybridizations described for each group unlike for the bonding type information where each group contained sets for three bond orders the first line under each group label must begin with the number of hybridizations described for that group after any number of spaces The next line dictates a hybridization for the bonded elements about to be described Hybrid ization labels must start with five spaces followed by one of the following character strings S hybridization p hybridization d hybridization sp hybridization Sp2 hybridization Sp3 hybridization sp3d hybridization sp3d2 hybridization Jaguar 7 0 User Manual 257 Chapter 9 Other Jaguar Files 258 For each hybridization the bonded elements with that hybridization are then listed in two lines the first indicating the number of elements and the second indicating the elements themselves as for the bonding type information Information for any following atoms should be preceded by a line with three asterisks and a blank line indi
78. Theor Chim Acta 1998 99 366 diffuse functions for rare gases extrapolated from those for the other elements in the row Hamilton T P Pulay P J Chem Phys 1986 84 5728 Pulay P J Comput Chem 1982 3 556 Pulay P Chem Phys Lett 1980 73 393 Jaguar 7 0 User Manual 329 References 330 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 Obara S Saika A J Chem Phys 1986 54 3963 Gill P M W Head Gordon M Pople J A J Chem Phys 1990 94 5564 Gill P M W Head Gordon M Pople J A Int J Quantum Chem 1989 23 269 Head Gordon M Pople J A J Chem Phys 1988 59 5777 Murphy R B Messmer R P J Chem Phys 1993 98 10102 For information on Molden see the Molden web site http www caos kun nl schaft molden molden html Stewart J J P MOPAC 6 QCPE 455 Hohenberg P Kohn W Phys Rev B 1964 136 864 Kohn W Sham L J Phys Rev A 1965 140 1133 Parr R G Yang W Density Functional Theory of Atoms and Molecules Oxford New York 1989 Density Functional Methods in Chemistry Labanowski J K Andzelm J W Eds Springer Verlag Berlin 1991 Colle R Salvetti O J Chem Phys 1990 93 534 Kraka E Chem Phys 1992 161 149 Audi G Wapstra A H Nuclear Phys 1995 A595 4 409 Cs sz r P Pulay P J Mol Struct 1984 1
79. a comment identifying each bond order The group is a list of bonded atoms and bond orders for the element being described for example Group 2 for carbon could describe C C and C O bonds by specifying that for bond order 2 Group 2 contains two elements with atom numbers 6 and 8 The first line under each bond order label must list the number of elements in the group for that bond order 2 for the example if this number is nonzero the next line must list the atomic numbers for those elements 6 and 8 in the example Here is the beginning of a sample lewis file illustrating a list of bonding type information for carbon including some comments to further explain the file format CALCULATION TYPE 01 HF DFT GVB BONDING TYPE 01 INFORMATION 6 CARBON Group 1 C H bonds only Group must be here the rest is a comment Bond order 1 this should be a non blank comment line 1 element 1 the atomic number of H Bond order 2 this should be a non blank comment line 0 elements Bond order 3 this should be a non blank comment line 0 elements Group 2 C C and C O bonds Bond order 1 0 elements Bond order 2 2 elements 6 8 Bond order 3 0 elements The number of spaces at the beginning of the lines described above is irrelevant for all lines except the Group lines After all the groups have been specified for a particular atom the file should contain a line containing three asterisks to indicate the next element
80. a previous job as described in Section 6 5 on page 136 Jaguar automatically uses the Hessian provided in your input file If you want to provide an initial Hessian in the input file choose Other from the Initial Hessian option menu If your input file does not contain a Hessian you can use the Initial Hessian option menu in the Optimization tab to specify what kind of initial Hessian Jaguar should generate You can select Keyword dconv in the gen section Keyword iaccg 2 in the gen section Keyword iaccg 3 in the gen section Keyword maxitg in the gen section Keyword inhess 2 in the gen section gov QN nde Jaguar 7 0 User Manual 69 Chapter 4 Optimizations and Scans 70 from among several internal guesses the Fischer Alml f Hessian 65 the Schlegel Hessian 66 or the unit matrix For most cases the Schlegel or Fischer Alml f options are the best choices The Schlegel guess is the default The final option Quantum mechanical is to have Jaguar compute the initial Hessian This calculation is the most time consuming of the initial Hessian options Theoretically it is the best option for cases where the other Hessian choices are inadequate although in practical terms other steps taken to improve optimizations are likely to be more cost effective 4 1 3 Coordinate Systems The coordinate system you choose for optimization can have a substantial impact on the convergence of the optimization The id
81. and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory J Am Chem Soc 1994 116 11875 Murphy R B Beachy M D Friesner R A Ringnalda M N Pseudospectral Local ized MP2 Methods Theory and Calculation of Conformational Energies J Chem Phys 1995 103 1481 Lu D Marten B Cao Y Ringnalda M N Friesner R A Goddard W A III Ab initio Predictions of Large Hyperpolarizability Push Pull Polymers Julolidinyl n isox azolone and Julolidinyl n N N diethylthiobarbituric acid Chem Phys Lett 1995 242 543 Cao Y Friesner R A Molecular hyper polarizabilities computed by pseudospectral methods J Chem Phys 2005 122 104102 Cao Y Beachy M D Braden D A Morrill L A Ringnalda M N Friesner R A Nuclear magnetic resonance shielding constants calculated by pseudospectral methods J Chem Phys 2005 722 224116 Murphy R B Pollard W T Friesner R A Pseudospectral localized generalized M ller Plesset methods with a generalized valence bond reference wave function Theory and calculation of conformational energies J Chem Phys 1997 106 5073 Vacek G Perry J K Langlois J M Chem Phys Lett 1999 310 189 Bobrowicz F W Goddard W A III Chapter 4 In Modern Theoretical Chemistry Methods of Electronic Structure Theory Schaefer H F II Ed 3 Plenum New York 1977 BIOGRAF manual MacroModel manual Jag
82. and is written to the output file jobname out For example here is the final output file for methylamine Jaguar 7 0 User Manual 315 Chapter 13 The pK Prediction Module 316 Table 13 2 File suffixes for pKa calculations Suffix Job Step Explanation dft_h B3LYP 6 31G geometry optimization for conjugate acid nrg_h B3LYP cc pVTZ f single point energy for conjugate acid solv_h B3LYP 6 31G single point solution phase calculation for conjugate acid pr _h input file preparation runs for conjugate acid dft B3LYP 6 31G geometry optimization for conjugate base nrg B3LYP cc pVTZ f single point energy for conjugate base solv B3LYP 6 31G single point solution phase calculation for conjugate base prt input file preparation runs for conjugate base Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module This molecule was recognized as a primary amine Correction factors have been applied and have an RMSD of 0 5 The pKa for methylamine is 10 3 13 4 6 Choice of Initial Geometry It is very important to choose the lowest energy conformer for the pK calculations As ab initio geometry optimizers only find the local minima for flexible systems long n alkyl chains many rotatable bonds we strongly suggest first running a conformational search with MacroModel for example to determine the global minimum energy structure which can then be used as an initial structure for the pK run
83. and the second a real number indicating f the number of electron pairs in each orbital of that shell The next line should contain the a terms for any orbital in the shell where j lt i and is not a core orbital Jaguar 7 0 User Manual 231 Chapter 8 The Jaguar Input File 232 The last line describing the shell lists all b terms for any orbital in the shell where j lt i and j is not a core orbital 8 14 The orbman Section The orbman section allows you to reorder orbitals in the guess section of a restart file or to form linear combinations of orbitals The format of the orbman section is as follows amp orbman hfiglcmo 14 3 3 k 1 B end amp where i j k and are integers indicating the ith jth kth and th orbitals before mixing Oe X Xj Xe and Xj and and B are angles in degrees indicating the degree of mixing The command hfiglcmo mixes the orbitals to form orbitals x74 7 xi according to the following equations new and x new X Xjcosa X sino new X XjcosQ X sino n 7 X cosp x sinp Xr x cosB x sinp Note that an angle of 90 permutes the two orbitals reversing the sign of one Each combination operation is performed independently and the operations are performed in the order they are listed in the orbman section Each rotation involving a previously altered orbital uses the new transformed orbital generated by the earlier operations Af
84. angle in a Hessian refinement O1 H2 O1 LE H3 O1 1 1 H2 108 0 or o1 H2 O1 ohbond H3 O1 ohbond H2 108 0 ohbond 1 1 28 Keyword nhesref 3 in the gen section Jaguar 7 0 User Manual 79 Chapter 4 Optimizations and Scans 80 Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refine ment For example for the second water input example shown above only two coordinates will actually be refined the O H bond distance which is the same for both bonds and the H O H angle The same would be true for the first example if molecular symmetry were used 4 4 Geometry Scans Geometry scans are a series of jobs run with input files that vary only in the value of one or more variables used to define an internal or Cartesian coordinate in the input structure You can perform a relaxed scan finding minimum energy geometries while holding one or more coordinates fixed to various values or a rigid scan varying only the scan coordinates To scan over a coordinate you must first define the coordinate as a variable then define the values that the coordinate must take You can set up geometry scans from Maestro or you can create an input file with the appropriate sections 4 4 1 Setting up Scans in Maestro To set up a scan from Maestro choose Relaxed coordinate scan or Rigid coor
85. atomic centers orthogonalized to the occupied space Another critical advan tage of LMP2 as for other localized correlation methods such as GVB and GVB RCI is that one can very precisely control which region of the molecule is correlated reducing CPU costs enormously The method has been shown to yield an accuracy for relative energies that is if anything superior to conventional MP2 due to elimination of basis set superposition error 60 However localized MP2 implementations in conventional electronic structure codes have not yet led to substantial reductions in CPU time since the first few steps of the necessary four index transformation are unaffected by localization of the occupied orbitals and the localized orbitals have tails that extend throughout the molecule We have carried out extensive tests demonstrating the accuracy and computational efficiency of the pseudospectral implementation of LMP2 as detailed in ref 16 In the pseudospectral approach we assemble two electron integrals over molecular orbitals directly and are thus able to fully profit from the huge reduction in the size of the virtual space in Pulay s theory Formally the PS implementation of LMP2 scales as nN however various types of cutoffs and multigrid procedures can reduce this to N In fact for calculations involving both the 6 31G and Dunning cc pVTZ basis sets we find a scaling N with system size The physical idea behind the LMP2 method is tha
86. atoms is not the optimal choice when the orbitals are delocalized as they are in aromatic systems such as benzene Such delocalized orbitals are represented in valence bond theory by resonance struc tures To handle aromatic systems you can delocalize the LMP2 pairs over neighboring atoms in the ring partial delocalization or over the whole ring full delocalization These options are available from the Resonance menu This feature is only available for aromatic rings of 6 or fewer atoms 45 Keyword loclmp2v 1 in the gen section 46 Keyword loclmp2v 3 in the gen section 47 Keywords iheter 1 in the gen section 48 Keyword ireson 1 in the gen section 49 Keyword ireson 2 in the gen section Jaguar 7 0 User Manual Chapter 3 Options Jaguar jaguar n Use structures from Workspace included entries 4 Molecule Theory scr Properties Solvation Output Level of theory GVB a GVB GVB Pairs All atom pairs Hetero atom pairs Job GVB 6 31G Single Point Energy Frequencies Start Read Write Edit Reset Close Help Figure 3 4 The Theory tab showing GVB controls 3 6 Generalized Valence Bond GVB Settings The GVB option of the Level of theory option menu allows you to request a Generalized Valence Bond Perfect Pairing GVB PP 22 calculation and to set the GVB pairs for that calculation The theory behind GVB calculations is exp
87. can be visualized using the surface display options in Maestro Orbital surfaces can be generated only for SCF and GVB wave functions MP2 calculations do not generate natural orbitals that could be used for surfaces For GVB wave functions surfaces are generated for the natural orbitals You can generate data for all surfaces in the same run The data for each surface is written to a separate vis file You can generate surfaces for each point in a geometry scan and orbital data The data for the property volume data is tabulated on a three dimensional rectangular grid The box containing the grid encompasses the van der Waals radii of all atoms in the molecule You can adjust the box size within the range 1 to 25 A and you can change the density of grid points within the range 1 25 points A using the Box size adjustment and Grid density text boxes in the Surfaces section 98 Keyword press in the gen section 99 Keyword tmpini in the gen section 100 Keyword tmpstp in the gen section 101 Keyword ntemp in the gen section 102 Keyword ip28 2 in the gen section 103 Keyword iplotesp 1 in the gen section 104 Keyword iplotden 1 in the gen section 105 Keyword iplotspn 1 in the gen section 106 Keywords iorb1a iorb2a iorb1b iorb2b in the gen section 107 Keywords xadj yadj zadj in the gen section 108 Keyword plotres 1 in the gen section Jaguar 7 0 User Manual 63 Chapter 3 Options 64 Jaguar
88. coefficients for this expansion are solved iteratively using a self consistent field method as for Hartree Fock However DFT includes exchange and or correlation density functionals within the Fock matrix used for the SCF procedure For DFT calculations the Hartree Fock exchange term K in the Fock matrix is replaced by the exchange correlation potential matrix elements E xe d Of lp Vp Fg Jl Neen f DOES ML i uxj 27 where f p Vp is an exchange correlation functional and y is Vp Vp The exchange correlation functional f p Vp is usually separated into exchange and corre lation functional components that are local or non local in the density fp Vel Gol f wulp Vol fol f wlp Vpl 28 Under the local density approximation LDA the non local functionals f y p Vp and f uL Ip Vpl are ignored when either or both of these terms are included the generalized gradient approximation GGA also known as the non local density approximation NLDA applies The local and non local exchange and correlation functionals available within Jaguar are described in Section 3 3 on page 35 and its references The electronic ground state energy E is given by lv i E Zu w far V pr 47e far f p Vpl 29 in Hartree atomic units where MN is the nuclear potential and J is the Coulomb potential Therefore for a given exchange correlation functional it is possible to solve iteratively for Kohn Sham orbitals y r and th
89. conformations This approach should be more accurate than that described in a although how important statistical effects are in practice remains to be ascertained 13 2 2 Equivalent Sites Some molecules have two or more equivalent sites for protonation or deprotonation Examples include ethanediamine the analogous dicarboxylic acid or the molecule melamine which has three equivalent sites In this situation a statistical correction factor arises from increased entropy of the appropriate species Jaguar does not automatically recognize equivalent sites so you must make this correction by hand to the result obtained from running the pK prediction module The correction factor is log N where N is the number of equivalent sites and the power of 2 comes from the fact that there are two particles involved H and the species being protonated The correction factors for two and three equivalent sites 298 K are 2equivalent sites bases 0 60 acids 0 60 e 3 equivalent sites bases 0 95 acids 0 95 The CH acid parameters include this correction so it should not be added in for CH acids Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module 13 2 3 Multiple Protonation Sites Many molecules have several sites which can have different pK values Consider a case with two distinct possible protonation sites for which we want to calculate the pK of site 1 Then the following situations are possible 1 The two
90. constraints Ve EEN 74 161 Jaguar 7 0 User Manual equivalent coordinates sse 73 for geometry optimization 11 14 70 72 160 179 frozen coordinates ss ssoe0se000e00e00e 71 161 harmonic niens 72 162 natural torsional angle 72 83 162 transition state searches seeeeeeeeeeeee 77 CONLOUT plots iu cased steve ero rre 84 convergence criteria geometry optimization 69 101 182 SCF energy aeea r 46 137 SCF energy keyword 193 solvation energy keyword 187 convergence problems troubleshooting 289 convergence schemes eeererrerrerrreeree 47 DIIS 47 120 keywords 193 194 OCBSE oen retten 47 120 coordinates Cartesian in geometry input constraining and freezing for refinement of Hessian TO CHOR ien tienes DEO redundant internal usse SCAM PI E Coulomb field charge fitting to Coulomb operator OU keyword for output ssssss obtaining i o information for 122 pseudospectral assembly of 142 143 counterpoise calculations 14 16 158 159 defining fragments Tor 221 Python Script for eene 219 specifying atoms Tor 222 coupled perturbed Hartree Foc
91. coordinates of the atoms in the geometry in angstroms The number of spaces you type does not matter as long as you use at least one space to separate different items When you finish entering the water geometry click OK To read in the structure click Read then navigate to the following directory SSCHRODINGER jaguar vversion samples where version is the 5 digit version number of your Jaguar software Select H20 in from the file list and click OK Whichever method of entry you chose the molecular structure should now be shown in the Workspace If you entered the geometry by hand the structure is a scratch entry You can run the job with a scratch entry but the results will not be incorporated into the Project Table unless you make it a named entry To do so click the Create entry from Workspace button in the toolbar and name the entry H20 Se When you finish setting up your calculation click the Start button The Start dialog box is displayed see Figure 2 6 on page 22 In this dialog box you can make settings for running the job In the Output section you can select an option for incorporation of results Choose Replace existing entries In the Job section you can provide a job name select the execution host the number of processors and the scratch directory The entry name H2O appears in the Name text box The names of the input output and log files for your job depend on the name you provide the Jaguar 7 0 User
92. copyright information 92 Jaguar data directory sess 237 Jaguar 7 0 User Manual 339 Index 340 Jag ar files neto es 237 Jaguar Panel eee 7 Jaguar programs esee 233 Jaguar Read dialog box sss 17 Jaguar Write dialog box sss 21 Jeer program uenerit nennen non 233 job directory local sss 23 27 JOD E sete 23 92 265 266 K killing jobs ierit 268 L launch eret 285 286 LDA see Local Density Approximation least squares operator Q description of 141 142 UE EE 47 Hessian keyword for 181 virtual orbitals keyword 196 Lewis dot structure keywords fOr scsacstscredaicadeitiessisateecdceeess 166 Jewnsflez nue e 237 setting GVB pairs from 166 setting van der Waals radii from 102 186 lewis file description and format 254 262 specifying in input file 155 Linear Synchronous Transit LST methods see QST guided transition state searches LMP2 method 40 42 149 152 counterpoise COIrections s s s 16 EU D 211 input file section see 218 key Words eee brennt 167 168 GUUPUE ITOID an ttem 97 98 pseudospectral implementation 1
93. covfac times the sum of their covalent radii which are listed in Table 8 46 The default value for this variable is 1 2 8 5 3 Molecular State Keywords Charge and Multiplicity The keywords that describe the input molecule s charge and spin multiplicity are shown in Table 8 3 These keywords correspond to GUI options described in Section 2 6 on page 18 Table 8 3 Keywords to describe the molecular state Keyword Value Description molchg any Overall charge on molecule excluding point charges set in pointch section default is 0 multip gt 0 Spin multiplicity 1 for singlet 2 for doublet etc default is 1 except Jaguar 7 0 User Manual for ihamtyp 0 when multip 2 by default Chapter 8 The Jaguar Input File 8 5 4 Atomic Mass Keyword The keyword massav determines the atomic masses used for any atoms whose masses or isotopes are not specifically set in the atomic section see Section 8 8 on page 219 The masses used are from ref 139 Table 8 4 Keyword to describe the atomic masses used Keyword Value Description massav 0 Use masses of most abundant isotopes as atomic masses 1 Use average isotopic masses as atomic masses where averages are weighted according to natural abundance of isotopes 8 5 5 Symmetry Related Keywords By default for most calculations Jaguar takes advantage molecular symmetry to reduce computing time as described in Section 2 7 2 on page 19 Several integer valued keywords sh
94. different conformation for each species The selection of the appropriate conformation can be nontrivial Our recommendation is to do a solution phase conformational search in MacroModel using the MMFF force field and the GB SA continuum solvent model This is a very fast procedure and gives a reasonable ordering of conformational free energies in solution Alternatively you can either construct the conformation by hand or use a gas phase conformational search Pre liminary results indicate that there are situations where a solution phase conformational search is necessary to obtain accurate results 2 Perform quantum chemical calculations for multiple conformations generated from a MacroModel solution phase conformational search and use all of this information to compute the pk Two ways of doing this are a Pick the conformer that has the lowest solution phase free energy for each protona tion state and compute the pK from this value This method is analogous to 1 above but allows for imprecision in the conformational search protocol It also takes more CPU time b Carry out a statistical mechanical average over conformations to determine the aver age pK The assumption made if this option is chosen is that the midpoint of the pK titration curve is achieved when the total population of the deprotonated state summing over all deprotonated conformations is equal to the total population of the protonated state also summing over all
95. each atom corresponding to the coarse medium fine ultrafine and gradient grids All coarse grids for 6 31G with or without the polarization functions indicated by the will set the boundary plane between atoms described earlier at the point where the grid point densities are the same for the two atoms because of the 1 flag Next seven shells apiece are specified for H atomic number 1 He atomic number 2 and Li atomic number 3 The actual default grid file continues with a list of coarse atomic grids for the other atoms in the basis set followed by the medium fine and ultrafine atomic grids in the same format before proceeding to define the grids for another basis set in the same manner The possible values of the numbers on the angular grid line are listed in Table 9 1 along with the corresponding number of points per angular shell and the degree of the highest spherical harmonic which the grid integrates exactly when relevant The full references are provided in a section beginning on page 323 Table 9 1 Number of points per angular shell and degree of the highest spherical harmonic exactly integrated by grids specified by various entries on the angular grid line Entry Points Degree Reference for Grid 1 6 3 Un 3 1 Stroud p 294 150 2 8 3 Un 3 2 Stroud p 294 150 3 12 3 U3 3 1 McLaren p 296 150 4 14 5 Un 5 2 Albrecht amp Collatz p 294 150 Jaguar 7 0 User Manual Chapter 9 Other Jag
96. each node should be the total number of processors available in the cluster For computer clusters that do use queuing software host entries must be included for each queue that is to be used and the value of processors for each entry should be the total number of processors available in the cluster See the Job Control Guide for details of the format for the schrodinger hosts file For all platforms you should use local disks for scratch space Performance is significantly reduced if an NFS mounted scratch disk is used Also avoid using scratch directories that are actually symbolic links Using symbolic links for scratch directories is known to prevent Jaguar jobs from running especially under Linux For example if scratch is actually a symbolic link to scr specify scr in the schrodinger hosts file rather than scratch 12 1 1 SGI IRIX mips4 and SGI Linux ia64 Altix Installations The minimum system requirements for SGI are Message Passing Toolkit MPT 1 6 0 0 for IRIX and 1 10 for Altix Array Services 3 5 for IRIX and 3 7 for Altix and Fortran runtime library 7 4 2m for IRIX The MPT and Array Services packages must be installed by the system administrator for your computer because the installation requires root permission For Altix both of these packages are installed from RPMs that are part of the SGI ProPack soft ware package For IRIX you can download these packages from http www sgi com products evaluation Following are
97. energy into Coulomb and exchange parts For each of these parts the contribution from each Hamiltonian is listed The highest occupied molecular orbital HOMO and lowest unoccupied molecular orbital LUMO energies are listed next Finally the energies for each occupied orbital and for the ten lowest energy virtual orbitals are provided with each orbital identified by a symmetry label Virtual orbitals and eigenvalues are determined in the same manner as in ref 128 The virtual orbitals are obtained by diagonalizing H gt f 2J K where fis the occupation of each orbital 1 for a closed shell For closed shell Hartree Fock calculations this definition yields the standard orbitals and eigenvalues Finally the CPU time for the job the machine upon which the job ran and its time of comple tion are noted at the end of the output file 5 3 Output File Content for Various Calculation Types Any time you make a non default setting for a calculation the output from the program pre notes the non default options chosen This output appears above the molecular geometry output from the pre program This section describes the changes in output for various calcula tion settings described in Chapter 3 Jaguar 7 0 User Manual Chapter 5 Output Generally only the format changes that result from these settings are discussed below Natu rally these settings will often change the data listed Options that have no significant impact on t
98. esolv0 value from input file as gas phase energy should yield same structure as nogas 0 2 For optimizations in solution skip gas phase geometry optimization and compute solvation energies using energy of initial structure as gas phase energy should yield same structure as nogas 0 intopt 0 Use Cartesian coordinates for optimization 1 Use internally generated redundant internal coordinates for optimization including any from coord or connect sections if they exist 2 Use internal coordinates from input Z matrix for optimization note if geometry input is in Cartesian format or contains a second bond angle rather than a torsional angle for any atom intopt is reset to 1 nmder 0 If calculating forces compute analytic derivatives of energy 1 If calculating forces compute numerical derivatives of energy obtained from calculations on 6 N tom perturbed geometries by moving each atom pertnd bohr in positive or negative x y or z direction 2 Calculate frequencies numerically needgwd 0 Do not compute DFT grid weight derivatives 1 Compute DFT grid weight derivatives and second derivatives if using CPHF 2 Compute DFT grid weight derivatives and gradient from grid translation symmetry will be turned off 3 Compute DFT grid weight derivatives and gradient from grid translation and rotation symmetry will be turned off maxitg gt 0 Maximum number of optimization iterations maximum number of structures generated default is 100 iacc
99. extrapolation noatcor 0 Analytic corrections calculated 1 No analytic corrections calculated nops 0 Use pseudospectral method to calculate J and K operators 1 Construct J and K from analytic four center two electron integrals no grid used noupdat 0 Fock matrix updating 147 set on or off automatically 1 No Fock matrix updating set iacc 1 if you set noupdat 1 iteravg 0 Do not average density matrices and adjust orbitals accordingly unless istavg keyword requests averaging gt 0 For iterations whose number is n iteravg 1 where n is an integer revise orbitals so that they correspond to average of density matrices from pre ceding and current iterations istavg 0 Do not average density matrices and adjust orbitals accordingly unless iteravg keyword requests averaging gt 0 For iterations whose number is lt istavg revise orbitals so that they corre spond to average of density matrices from preceding and current iterations noauto 0 Grid choice is automatic 1 All calculations done on coarse grid 2 All calculations done on medium grid 3 All calculations done on fine grid Jaguar 7 0 User Manual 195 Chapter 8 The Jaguar Input File Table 8 28 Keywords for methods used in the SCF convergence procedures Continued Keyword Value Description 4 All calculations done on ultrafine grid idenavg 0 Converge in the usual fashion 1 Do density averaging before DIIS starts mixing in some of old orbitals with new orbitals default f
100. file gau When this option is selected a file in the format of a GAUSSIAN input file is created with the suffix gau 3 The file information includes the molecular geometry the basis set name and the type of calculation to be performed as well as the molecular charge and the spin multi plicity of the molecule and any relevant effective core potential information If symmetry is turned off that setting will be entered into the gau file For GVB calculations you should specify GVB pairs Jaguar will also generate a GVB initial guess which will be included in the gau file For more information on setting up GAUSSIAN input files see Section 6 7 on page 139 GAMESS input file gamess To write out an input file for the program GAMESS you can select this option The resultant file s suffix will be gamess The file will include the molecular geometry the basis set and some information on the type of calculation to be performed as well as the molecular charge and the spin multiplicity of the molecule and any relevant effective core potential information SPARTAN archive file arc You can use this option to generate a SPARTAN 4 0 archive file with the suffix arc 12 Keyword ip8 2 in the gen section 13 Keyword ip160 2 in the gen section 14 Keyword ip168 2 in the gen section Jaguar 7 0 User Manual Chapter 5 Output XYZ file xyz If you set this option Jaguar creates a file in XYZ format with the
101. for parallel execution is nproc and must be either 1 or 2 If you select two processors the acid and base sections of the job are initiated as separate Jaguar jobs Selecting more processors does not run the separate Jaguar jobs in parallel If you want to run more than one pK job with a single command you must use the jaguar batch command and specify pka bat as the batch file jaguar batch options pka bat jobnamel jobname2 The input files for the pK jobs must be in the format described above Use of the wildcard in job names is allowed You cannot specify separate protonated and deprotonated species with the batch command The command options are described in Chapter 10 13 4 5 Monitoring pK Calculations The pK calculations can be monitored from the Maestro Monitor panel or by looking at the file pka blog where is a process identification number For each molecule Jaguar creates a jobname_pka subdirectory in the local directory and writes the input and output for each job step there The input and output filenames have suffixes appended to jobname that explain what is calculated in each step These suffixes are listed in Table 13 2 The energies of the gas phase optimized structures and the solvation energies for the proto nated and deprotonated forms are extracted from the output files and written to a file named jobname jres in the jobname_pka directory The pK value is then calculated from the data in this file
102. from previous runs and some tips on using both Jaguar and GAUSSIAN Chapter 7 describes some of the theory behind the pseudospectral method and the electron correlation methods used in Jaguar This chapter includes information on pseudospectral implementations of GVB and local MP2 techniques and a brief description of density func tional theory Jaguar 7 0 User Manual Chapter 1 Introduction Chapter 8 describes the Jaguar input file in detail You may find this chapter especially useful if you want to run some jobs without using the GUI Chapter 9 describes other Jaguar files that are necessary for calculations You may skip Chapter 8 and Chapter 9 if you want to run all jobs from the GUI but you might want to skim them anyway to find out more about Jaguar and the methods it uses Chapter 10 provides information on submitting jobs from the command line and running multiple Jaguar jobs using batch scripts Chapter 11 contains troubleshooting hints concerning various problems you might encounter especially when first setting up Jaguar on your system Chapter 12 contains information on running calculations on parallel computers Chapter 13 describes the pK calculation module 1 2 Running Schrodinger Software To run any Schr dinger program on a Unix platform or start a Schr dinger job on a remote host from a Unix platform you must first set the SCHRODINGER environment variable to the installation directory for your Schr
103. from the transition state ircmax 6 Maximum number of IRC points to be found in any direction Must be a positive integer iremxcyc 30 Maximum number of geometry iterations to calculate each IRC point Must be a positive integer 1 2 1 2 ircstep 0 1 Step size taken for each IRC point in bohrs amu 4 or radians amu ircgcut 1 0 Scale factor for the cutoff that is used to determine whether the gradient is too small to locate the next IRC point Use values that are less than 1 ip472 0 Do not save the IRC structures in the mae output file 2 Save the IRC structures in the mae output file and write the reaction coordinate value as a property that performed a Hessian evaluation and symmetry is on the IRC calculation might not produce any points or might not produce points on the actual reaction path if the transition state has higher symmetry than the reaction path If this is the case you should turn symmetry off isymm 0 in the gen section If you evaluate the Hessian with inhess 4 in the gen section symmetry is turned off for analytic Hessian calculations and the subsequent IRC calculations are done without symmetry The IRC calculation can fail if the step size is too small The warning message states that the vector used to determine the step is too small You can increase the step size by setting ircstep in the gen section The IRC calculation can also fail if the potential energy surface is very flat and
104. if 2 a basis set function Otherwise the number should be 0 The rest of the numbers on that line determine the way that Jaguar will contract some of the functions and the range of each function The numbers before the dash describe how many of the functions are included in that contraction For example if there were two such numbers 2 and 1 the line would indicate that Jaguar would contract the first two Gaussians provided immediately below into one contracted function and would treat the third Gaussian as an uncontracted function If you want to add or change a basis set to a basis file you should probably contract together all Gaussians whose exponents are greater than 0 3 The default basis information gener ally follows this rule although there are some exceptions see the Li s and p function informa tion in the sample file below for an example The numbers after the dash describe the range of each such function There should be one such number for each contraction number before the dash A zero indicates that the contracted func tion will be treated as a long range function while a 1 2 3 or 4 indicate various types of short range functions These assignments help determine the symmetrization of the Fock matrix components by the side choosing method described in Ref 13 These range values are only used in pseudospectral calculations so if your basis set will be used for non pseudo Jaguar 7 0 User Manua
105. improve calculations of thermochemical properties which use the scaled frequencies In Jaguar two options are available for frequency scaling the Pulay et al Modified Scaled Quantum Mechanical Force Fields SQM method 75 for B3LYP calculations using the 6 31G basis set and standard frequency scaling in which all frequencies are simply multi plied by a single parameter The SOM method alters the frequencies by scaling the Hessian elements themselves in internal coordinates using 11 different scale factors which depend on the type of stretch bend or torsion This method was parametrized using B3LYP calculations for 30 molecules containing C H N O and CI using the 6 31G basis set Jaguar permits the SOM scaling method to be used only for B3LYP 6 31G frequency jobs You can turn on SOM scaling by selecting Pulay SQM method B3LYP 6 31G factors The method is off by default Alternatively for any type of frequency job you can multiply all frequencies by the same scale factor by selecting Scaling factor and selecting a combination of method and basis set from the option menu or selecting User defined from the option menu and entering a factor in the text box Table 3 4 lists the recommended scale factors for various methods and basis sets These factors are used when you make a selection from the option menu The factors in the table are from Ref 76 and are optimized for the best agreement with experiment for the frequencies t
106. in IRC calculations 86 185 key Words c nee o to dee ite entes 165 Maestro options ssee 29 30 orbital populations eee 48 output Information 92 specifying for GAUSSIAN input 140 use of in calculation 19 20 synchronous transit quasi Newton methods see QST guided transition state searches T TDDFT caleulapons 35 176 temperatures for thermochemical calculations e EE 191 lr KEE 115 SEMINE esse 63 temporary directory eene 24 287 after job is Klled ss 268 errors related to 286 287 inobtput Me sissies A vats pea nobles 92 saving at end Of job 267 temporary files sidere io 268 saving at end of job 267 Theory tabs i adierit 36 41 43 thermal emearng eee 47 197 thermochemical properties 62 63 keywords eee tette 191 lr EE 115 time stamps in log file option for 267 timex e 234 timing information key WOT iaceo eie ete s 204 Maestro option 122 torsional angles freezing all aient eee 179 TW Z matfix i n ie eee eee te 12 transition metals improving convergence 45 133 134 initial guess for 131 132 134 227 Transition State ob 76 transition vector cessere 75 184 transition state optimization 67 80 constraining bond lengths or angles 70 74 converge
107. in the jaguar babel command are used as they are If you omit the output file name or if you give CON as the output file name the output is written to standard output You can add hydrogen atoms to a structure when you do a conversion using the h option and you can delete hydrogen atoms from a structure using the d option Babel can convert multi structure files to other multi structure files or to a set of single struc ture files You must supply both an input file name and an output file name if you are converting a multi structure file You can select the structures to convert by specifying the range input argument A valid ranges is in the form numberl number2 or the word a11 to select all structures The quotes are required For Jaguar output files the last structure is converted if no range is given otherwise the first structure is converted by default To generate a set of single structure files use the split keyword The names of these files have a four digit index number inserted before the file extension For example to write indi vidual Jaguar input files Cartesian for the 5th through 10th intermediate structures in a Jaguar geometry optimization run type the command jaguar babel ijagout job out 5 10 0jagc iter in split The files iter0001 in iter0002 in iter0006 in are written by Babel Jaguar 7 0 User Manual 269 Chapter 10 Running Jobs Table 10 3 Input format keywords and file types for b
108. integer values are limited to a small set which differs for each keyword Real values can optionally include a d or e floating point power of ten Character string keyword values may be limited to a small set as for a basis set descrip tion or may allow a general string like a file name Each section is delineated by a pair of amp or characters The section name follows imme diately after the first amp or Thus for example the general keyword section may begin with amp gen or Sgen and ends with amp or Within the gen section allowed keywords are followed by numerical arguments giving their values whose meanings are explained in Section 8 5 on page 163 At least one spacing character must precede and follow each keyword or keyword value pair Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 1 Sections for Jaguar input files Section Description zmat Contains list of atomic coordinates describing molecular geometry in Cartesian or Z matrix format zvar Sets values for zmat section variables coord Specify particular internal coordinates to be used for optimization connect Specify particular internal coordinates to be used when generating coordinates for opti mization tvec Specify reaction coordinate at transition state for IRC calculations gen Sets general control keywords including those describing the calculation performed the grids deali
109. integrals esse 93 energy contributions 103 105 open shell singlet keyword 199 open shell systems energy contributions in output 96 keywords inii hinten 194 Optimization ob 68 optimizations see geometry optimization orbital energies in output sees 96 orbitals ee Oh 232 fixing symmetry populations 48 information in output 93 98 keywords for output of 207 210 output options 125 128 lu 63 65 printing for guess section 229 Ieorderitg 2 rae ener 232 e 63 order of Jaguar programs run specifying 233 235 ordering of dealiasing functions 245 organometallics improving convergence dE 131 132 133 134 output file echoing input file mm 233 Jaguar 7 0 User Manual 341 Index 342 location ertet eod 5 21 reference in log file 129 standard output settings 121 124 summarizing eee 87 92 output file information Dt 117 convergence methods other than DIIS 120 DFT calculation options 97 frequency IR and thermochemistry calculati iis 2 orantis 114 geometry and transition state optimizations sissie iaei 99 GVB calculations eee 98 LMP calculation options
110. into the of Processors window in the Jaguar Run panel By default the maximum number of processors that you can request is shown in this window The number is read from the processors line for the selected host in the schrodinger hosts file Jaguar 7 0 User Manual 301 Chapter 12 Parallel Jaguar 302 If you need to pass additional parameters to the POE or MPI launch commands you can set the environment variable SCHRODINGER_MPI_FLAGS to the arguments that you want to pass in For example for verbose output from mpirun on an SGI set the following environment variable csh tcsh setenv SCHRODINGER MPI FLAGS v sh ksh bash export SCHRODINGER MPI FLAGS v When a parallel job is run on an IBM host the following POE flags are automatically set euilib ip shared memory yes wait mode poll You can tell whether a job is running in parallel by looking at its log file jobname 10g If the job is running in parallel the third line of the log file will contain for example Running on 2 processors If there is no such line the job is running in serial mode If you are using a queueing system for your parallel jobs note that the number of processes created by Jaguar is the number of processors for the job plus one because the Jaguar control program jexec always runs as a separate process Also to ensure that the path to mpirun is specified when the job is actually run you can prepend the path to mpirun to the PATH e
111. ira rwr irb amp You must also set irder 1 isymm 0 and ifreq 1 The ifreq setting is necessary to force tight accuracy in the SCF but no frequency calculation is actually performed To compute partial frequencies for a fragment you must first define the fragments in the atomic section then make the setting freqfrag fragno in the gen section of the input file for the frequency calculation These settings are in addition to any other frequency related settings 8 5 16 Basis Set Keywords The character string keyword basis allows you to override the default basis set 6 31G This keyword should be a string describing the standard basis and any desired polarization and diffuse functions The string describing the standard basis should be chosen from the first column of Table 3 1 on page 32 or Table 3 2 on page 34 Lowercase or uppercase letters can be used The polarization and diffuse function options are described by adding or immediately after the basis name The meaning of these symbols is also described in Section 3 2 on page 30 Neither polarization nor diffuse functions are used if none of these options are specified The tables in Section 3 2 list the basis sets and indicate which options and atoms Jaguar currently accepts for each The other keyword relating to the basis set numd allows you to choose whether to use five or six d functions in each d shell If you do not set numd explicitly the number of d functions is
112. is 2 the ultrafine grid is used and that three cutoff values which differ from the defaults follow The next three lines set the cutoff values cut21 cut22 and cut24 If you need more information on cutoffs contact Schr dinger The variables jcor and kcor determine what analytic corrections are calculated for a particular SCF iteration The meanings of their possible values are shown in Table 9 2 The variables a b and c in the table refer to distinct atoms To perform an all analytic calculation you can set the keyword nops in the gen section of the input file to 1 All analytic calculations use the cutoff keyword values in the cutoff file but ignore the jcor kcor and pseudospectral grid information Jaguar 7 0 User Manual 253 Chapter 9 Other Jaguar Files 254 Table 9 2 Determination of calculations of analytic corrections for SCF iterations Variable Value Description jcor 0 No Coulomb terms calculated analytically 1 Atomic analytic corrections of the form lt aalaa gt calculated for J 3 Analytic corrections of the form lt aalaa gt and lt aalbb gt calculated for J 4 Analytic corrections of the form lt aalaa gt lt aalab gt lt aalbb gt and lt aalbc gt calculated for J 5 Analytic corrections of the form lt aalaa gt lt aalab gt lt aalbb gt lt ablab gt and lt aalbc gt calculated for J diatomic lt aalbc gt kcor 0 No exchange terms calculated analytically 1 Atomic analyti
113. jobs The output lists the job ID the job name the status Kill the specified Jaguar jobs or all jobs that have the specified status This command is processed immediately Remove records for the specified jobs from the job database If no jobname is given all completed jobs are purged Stop the specified Jaguar jobs or all jobs that have the specified status when the currently running executable has finished Report the hardware and software configuration This command gives the same output as the SCHRODINGER machid com mand Report information on the hardware platform This command gives the same output as the SCHRODINGER plat form com mand List the available batch scripts Report any system requirements for Jaguar and whether they are met Display a command syntax summary including a list of valid commands Chapter 10 Running Jobs The jobnames argument to the jaguar command is a list of names Each name in the list is the name of a Jaguar job that is run and each name also specifies an input file The name can be given with or without a in extension If the in extension is given Jaguar removes it to form the job name If the in extension is not given Jaguar adds it to form the input file name For example the commands jaguar run bio jaguar run h2o in both run a Jaguar job with the job name h2o and the input file h2o in The job control functions of the jaguar command jobs kill stop and purg
114. keywords and run them through Jaguar SJOB S JOB protol Jaguar 7 0 User Manual Chapter 10 Running Jobs Now go back to the original launch directory create the directory for protocol2 and repeat the calculations using protocol 2 OPTIONS basis cc pvtz dftname x3lyp icfit 1 WORKDIR protocol2 OUTDIR protocol2 JOB SJOB proto2 To run this script for the files in the subdirectory structures you would use the command jaguar batch template bat structures in The input files are copied from the structures to the directory specified by WORKDIR modi fied with keywords and renamed as specified in the batch script and then submitted to Jaguar The output file the log file and the restart file are written to the directory specified by OUTDIR 10 2 4 Using Python Scripts with jaguar batch In addition to Jaguar batch scripts the jaguar batch command also accepts a Python script as the batch script You can only run jaguar batch with a Python script from the command line The Python package provided with Schr dinger software provides Python language extensions to analyze and manipulate structures including reading and writing a variety of file formats interfaces to Maestro including support for creating customized user interfaces and functions to interface with the Schr dinger Job Control facility For more information see the document Scripting with Python The Jaguar software distribution includes two Python
115. line contains information for one grid point the electrostatic potential value in hartrees the coordinates of the grid point in bohrs and if ip172 3 the grid weights 8 5 23 Output Keywords for Each Iteration The information in Table 8 34 concerns output which can be printed out every SCF iteration if the keyword is set to 2 The information is not printed if the keyword is set to 1 The option ip152 is the only one whose default value of 1 indicates that it is on When ip152 is set to 1 the file restart in is created in the temp directory for the job at the end of the last completed iteration overwriting the restart in file created from the previous iteration This input file can then be used to restart the calculation To turn off ip152 you must set it to 0 8 5 24 Orbital Output Keywords Orbital information can be printed out as well The orbital keywords determine what orbitals are printed in the output at what stage they are printed and the format Jaguar 7 0 User Manual 207 Chapter 8 The Jaguar Input File 208 Table 8 34 Effect of setting output keywords for each iteration to 2 Keyword Description of What Is Printed When ipi 2 ip15 DUS coefficients ip17 Energy components ip110 Density matrix if Fock matrix updating was not performed during that iteration or density difference matrix if Fock matrix updating was done ip121 All J and K matrices in atomic orbital space ip122 Fock matrix in a
116. line types in a batch input file are illustrated in the sample files in the next subsection Directions on how to submit a batch job follow in the final subsection 10 2 2 Running jaguar batch You can start Jaguar batch jobs from Maestro or from the command line Maestro automati cally creates a simple batch job when you specify multiple structures as input to any Jaguar task See Section 2 10 on page 24 for more information on using Maestro to run batch jobs The syntax of the jaguar batch command is jaguar batch command options batchfile bat joblist If the batch script batchfile bat uses JOB in job specifications you must supply the list of jobs to substitute in joblist In the command the suffix bat is optional if it is missing it is added to the stem batchfile The Job Control options REL VER HOST USER and WAIT and the jaguar run option PROCS can be used in the jaguar batch command For distributed batch jobs you can specify a list of hosts with the HOST option The host names in the list must be separated by spaces and if there is more than one host the list must be enclosed in quotes If a host has more than one processor you can select multiple processors either by repeating the host name or by appending a colon and the number of processors to the host name e g cluster 32 There are also some unique command options for the jaguar batch command which are summarized in Table 10 6 Jaguar 7 0 User M
117. lone pairs on an atom should be specified as GVB lone pairs and these GVB lone pairs should be identified by consecutive numbers starting with 101 Thus if the molecule had one lone pair on atom 2 and two on atom 5 the lines describing them would contain the numbers 101 2 2 101 5 5 and 102 5 5 Three more entries may be added onto the ends of all of the lines specifying the pairs these entries are present in new input files generated during or after calculations The first value if it is present is either 0 or 1 where a O entry is a place holder and a 1 entry indicates that a restricted configuration interaction RCI calculation including that pair will be performed By default the pair will not be included in an RCI calculation The next two values if they exist give the CI coefficients for the first and second GVB natural orbitals in each pair The first coefficient should always be positive and its magnitude should always be greater than that of the second coefficient which should always be negative These coefficients are included in new input files so that if you restart the calculation with the new input file the contributions of each GVB natural orbital are known The sample gvb section that follows sets a sigma bond pair with RCI on between atom 1 and atom 2 and two lone pairs on atom 1 Jaguar 7 0 User Manual 217 Chapter 8 The Jaguar Input File 218 8 7 The Imp2 Section The Imp2 section whose
118. metals sometimes for other atoms beyond Ar 3 Quick mixed grid types looser cutoffs iacscf 0 Make no special adjustments variable vshift cutoff adjustments etc for convergence 1 Start with level shift vshift of 5 0 and decrement over 10 iterations to 0 8 remove overlap eigenvectors if their associated eigenvalues are less than 5e 3 keep number of canonical orbitals fixed during optimization run at ultrafine accuracy level and with tight cutoffs 2 Start with level shift vshift of 6 0 and decrement over 12 iterations to Jaguar 7 0 User Manual 0 8 vary level shift during run by raising it when SCF is restarted here when the energy rises by 0 0001 au Chapter 8 The Jaguar Input File Table 8 28 Keywords for methods used in the SCF convergence procedures Continued Keyword Value Description 3 Use extreme cutoffs maximal analytic corrections while still allowing medium pseudospectral grids for some iterations 4 Same as iacscf 1 except with maximal analytic corrections retryscf 0 Do not retry SCF if convergence failure is detected 1 Retry SCF with iacc 1 and vshift 1 0 if a convergence failure is detected noabortscf 0 Abort SCF if checks indicate convergence failure 1 Ignore checks that would abort the SCF before it has reached the maxi mum iterations jksep 0 2J K formed for core when convenient 1 J and K for core are kept separate maxdiis 10 Number of Fock matrices to use in DIIS
119. methods to guide transition state search Sets itrvec to 5 qstinit 0 5 Distance of LST transition state initial guess between reactant and prod uct geometries Range is 0 0 to 1 0 ifollow 0 For each optimization iteration select a new eigenvector to follow 1 For each optimization iteration follow eigenvector that most closely correlates with one followed previously itrvec 0 Select lowest Hessian eigenvector as transition vector gt 0 Select eigenvector number itrvec as transition vector see Section 4 3 on page 74 Sets ifollow to 1 Jaguar 7 0 User Manual 179 Chapter 8 The Jaguar Input File 180 Table 8 18 Keywords for transition state optimizations Continued Keyword Value Description 1 Select lowest non torsional eigenvector as transition vector 2 Select lowest stretching eigenvector as transition vector 5 Select eigenvector which best represents reaction path Table 8 19 Keywords for control of the Hessian Keyword Value Description inhess 1 Use Fischer Alml f guess for Hessian 0 Use Schlegel guess for Hessian default choice only if no hess section exists 1 Use unit matrix for initial Hessian 2 Use Cartesian input Hessian found in hess section inhess 2 automati cally if non empty hess section exists 4 Compute and use quantum mechanical Hessian irefhup 2 Refine initial Hessian using Powell updates 140 3 Refine initial Hessian using mixed Murtagh Sargent Powell updates 141 4 Refin
120. optimizations solvation calculations charge fitting and all other calculations and properties available for Hartree Fock wave functions DFT calculations are selected by choosing DFT Density Functional Theory from the Level of theory option menu in the Theory tab When you make this choice controls for DFT calcula tion are displayed below this menu If you are doing calculations for an open shell molecule you can run a spin restricted RODFT or a spin unrestricted UDFT calculation The default is a spin restricted calcula tion To run a UDFT calculation select Spin unrestricted You can run calculations for excited states of a closed shell molecule using time dependent density functional theory TDDFT TDDFT has been implemented in Jaguar using the Tamm Dancoff approximation 30 To run an excited state calculation select Excited state TDDFT then enter the number of excited states in the Number of excited states text box You should select more excited states than you are actually interested in for two reasons The first is that the initial guess might not accurately reflect the final states and the second is to ensure that near degeneracies are accounted for You can also set the number of TDDFT iterations 5 Keyword iuhf 0 in the gen section 6 Keyword iuhf 1 in the gen section Jaguar 7 0 User Manual 35 Chapter 3 Options 36 Jaguar jaguar DIE Use structures from Workspace included entries
121. output keywords set to 1 24 Relevant orbital output keyword set to 2 3 4 5 or 6 in the gen section depending on the format setting chosen 25 Relevant orbital output keyword set to 7 8 9 10 or 11 in the gen section depending on the format setting cho sen 26 Relevant orbital output keyword set to 2 7 or 12 in the gen section depending on which orbitals are printed 27 Relevant orbital output keyword set to 3 8 or 13 in the gen section depending on which orbitals are printed 28 Relevant orbital output keyword set to 4 9 or 14 in the gen section depending on which orbitals are printed 29 Relevant orbital output keyword set to 5 10 or 15 in the gen section depending on which orbitals are printed 30 Relevant orbital output keyword set to 6 11 or 16 in the gen section depending on which orbitals are printed Jaguar 7 0 User Manual Chapter 5 Output Here are some examples of output for each of these style options The output shown is from output files generated from a calculation of water with a 6 31G basis set for occupied orbitals after the SCF iterations Only the first two occupied orbitals are shown in each case and not all functions are shown these gaps are indicated by For the Format option Large elements as f5 2 labels in list 1 Orbital Energy S 20 555133 Occupation 1 000000 Symmetry A1 Oo 0 99 2 Orbital Energy 1 345597 Occupation 1 000000 Symmetry A1 S S Z Oo 0 21 0 4
122. reaction coordinate for the IRC path is mass weighted whereas the reaction coordinate for the minimum energy path is not Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans Jaguar jaguar DIE Molecule Theory scr Optimization IRC Properties Solvation Output Direction Forward Reverse d Structures Transition state Bel Choose Reactant E o Choose Product zl Choose Number of IRC points 6 IRC step size 0 10 Maximum optimization steps per point 30 W Use mass weighted coordinates Jot Start Read Write Edit Reset Close Help Figure 4 4 The IRC tab IRC calculations can be set up from Maestro or by adding keywords to an input file see Section 8 5 12 on page 184 To set up an IRC or minimum energy path calculation from Maestro you must first perform a transition state calculation and read in the restart file then choose Reaction Coordinate from the Jaguar submenu of the Applications menu The calculation requires an accurate Hessian for the transition state You can precalculate the Hessian and read it in from the restart file or calculate the Hessian as part of the IRC or MEP calculation To read the Hessian choose Other from the Initial Hessian option menu in the 29 Keyword inhess 2 in the gen section Jaguar 7 0 User Manual 85 Chapter 4 Optimizations and Scans 86 Optimization tab
123. remaining functions are classified as long range func tions which are all considered to be in one single group 13 Since Q does not depend on the wave function itself it can be fully computed before the SCF procedure However since the Q for each grid type contains Npasis x Noiq elements where Nbasis is the number of basis functions and Nu the number of grid points which is generally larger than Nie we sometimes reduce memory demands by only computing and storing the Ny X Ng matrix S R wR in the program rwr for cases where the Q for that grid type is only needed for one SCF iteration We then assemble the full Q during the SCF iteration for which it is needed After the program rwr has generated the Q or S R wR matrix the program scf takes the initial orbitals and iteratively modifies them with the pseudospectral method until convergence This process involves calculating the values of the necessary integrals on the grid points and actually assembling the Fock matrix from the computed information The three center one electron pseudospectral integrals on the grid points are defined by 9 1 0 1 E a r 2 Vig Ig where Q and q are basis functions and the index g represents a grid point These integrals are calculated for all combinations of basis functions and grid points not eliminated by cutoffs and the Fock matrix is assembled from its Coulomb and exchange matrix components J i and K j which are calculated in physi
124. restart the calculation with the wave function and other data already calculated you can just read in the new input file The file name is jobname in where the asterisks represent a two digit number This number is 01 if the name of the input file for the job from which it was generated is not in this form and is otherwise set to the number after that assigned to the current input file These files overwrite any other existing files of the same name As an example if you run the job h2o the restart file generated during the run is called h20 01 in You could then read this file as described in Section 2 5 on page 17 and use it to continue on with the calculation possibly after making some changes to the calculation requested The new input file generated during this second run would be called h20 02 in If you want to start a new job where the previous job left off you need only read the new input file in then make any changes you think are necessary for example you could change the SCF energy convergence criterion in the SCF tab Similarly if you want to perform an addi tional calculation once a geometry has been optimized you can read in the restart file as input for the second job and make any necessary changes to it such as selecting a GVB calculation instead of Hartree Fock Section 2 5 on page 17 contains information on reading input files in the GUI See Chapter 8 if you would like more information on input files Note tha
125. run from structure files the results cannot be incorporated automatically You can select multiple structures as input for many kinds of Jaguar calculations When you do Maestro creates a Jaguar batch script that runs the calculation for each structure indepen dently These independent calculations can be run across multiple processors For more infor mation see Section 2 9 on page 22 Below the tabs is the Job text box in which a summary of the calculation type is displayed and below this text box is a row of buttons Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro Jaguar jaguar a Use structures from Selected structure files Files f zonel dyall 1 10 phenanthroline mae Browse Molecule Theory scr Properties Solvation Output Symmetry Use if present Molecular state w Use charge and multiplicity from Project Table Create Properties Use these values Molecular charge o Spin multiplicity 25 1 1 Basis set 6 31G Polarization 4 Diffuse None Number of D functions w 5D 6D 120 basis functions Job B3LYP 6 31G Single Point Energy Start Read Write Edit Reset Close Help Figure 2 1 The Jaguar panel Start Opens a dialog box in which you can make selections for running the job and incorporating the output and then start the job See Section 2 9 on page 22 Read Opens a file brow
126. run with a batch script are Multiple independent jobs with predetermined input files The same type of job for several input geometries A series of jobs in which later jobs use files generated during earlier jobs Several Jaguar batch scripts are included with Jaguar You can also write your own batch scripts or save job settings as a batch script in the Jaguar Write dialog box Maestro writes temporary batch scripts and runs a batch job whenever you run jobs with multiple structures as input that do not have geometry dependent settings Section 10 2 on page 272 provides details on batch scripts Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro _ Jaguar Run Batch File Script zone1 dya11 jaguar bz Browse Source of structures Selected structure files Files zone1 dya11 1 10 phen Browse For input files Use structure only ignore settings w Use both structure and settings Start Close Help Figure 2 8 The Run Batch File panel Jaguar batch jobs can be run from the Run Batch File panel which you open by choosing Run Batch File from the Jaguar submenu of the Applications menu To run a batch job you must select a script and a source of structures and start the job If you select Jaguar input files for the structural input you can choose whether to use or ignore the settings in the input files To select a script you can enter the path in the Scrip
127. scheme option menu in the SCF tab Generally DIIS is the better choice but the GVB DIIS convergence scheme sometimes leads to con vergence when DIIS does not The GVB DIIS scheme works by ensuring that each new Jaguar 7 0 User Manual Chapter 6 Using Jaguar set of occupied orbitals has maximum overlap with the previous set The advantage of this is that oscillations due to frequently changing occupations are damped The disad vantage is that if the initial guess occupies the wrong orbitals the SCF can converge to an excited state Set the SCF level shift in the SCF tab to 0 5 or 1 0 The higher the setting the more the energies of the virtual orbitals are increased before diagonalization and the more the mixing of the real and virtual orbitals is reduced High SCF level shifts can slow conver gence by several iterations but can often help otherwise intractable cases to converge Because jobs with SCF level shifts are slightly more likely to converge to excited states you may also want to restart these jobs without any SCF level shift As of Jaguar 7 0 a level shift of 1 0 is used automatically if Jaguar detects that the SCF is not converging If the calculation is a DFT job use finer DFT grids You can adjust this setting from the Grid density option menu in the Theory tab This setting also increases the computational cost Asa last resort try setting iacscf to 1 or 4 see Table 8 28 on page 194 for descriptions of these s
128. scripts jaguar v70018 scripts geopt dft I bat geopt dft II bat geopt dft III bat hydrogen bond py j2 bat ri E zg a Directory working Launch Jaguar Scripts Notes ar EI Selection 1e2 NB r2006 1 beta latest jaguar v70018 scripts Figure 2 9 The Select Batch Script panel Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro After you finish selecting the batch script and input files click Start to launch the batch job The Monitor panel opens and shows the batch log file blog for the batch job which logs the completion of each Jaguar job launched from the batch script The information is automatically updated as the Jaguar jobs run 2 11 Output A Jaguar log file contains comments on the progress of a job If the job was started from Maestro the log file is written to the local job directory The log file notes when each section of Jaguar is complete as well as noting data from each iteration in an SCF calculation as it is calculated You can view this file in the Monitor panel which is displayed when a job is launched or when you choose Monitor from the Applications menu in the main window See Section 5 7 on page 128 for more information on this file The primary Jaguar output is contained in the output file which is created in the scratch direc tory of the host on which the calculation is run and is copied back to the local host when the job finishes The outp
129. text editor make sure its format agrees with that described in Chapter 8 You can run a single Jaguar job from the command line with the command jaguar run jobname in where jobname is the stem of your input file name jobname in Jaguar supplies the in extension if you omit it With this command the job runs on the machine upon which you have submitted the command and uses the most recent version of Jaguar To run a Jaguar job on another machine use a command in this form jaguar run HOST hostname jobname Jaguar 7 0 User Manual Chapter 10 Running Jobs Table 10 2 Options for the jaguar run command Option Effect Default Behavior HOST Run a Jaguar job on the specified host or Run a Jaguar job on the local host hostname submit a Jaguar job to the specified batch queue Replaces h USER Specify the user name to be used for Use the same user name as on the job username remote jobs Must be used with HOST submission host WAIT Wait for the Jaguar job to finish before Return to the command prompt immedi returning to the command prompt ately Replaces w keepscr Keep temporary files and temp directory Temporary files are cleaned out of temp for job at end of job Replaces s directory and temporary directory is removed at end of job SAVE Copy temporary files ina zip file back Temporary files are cleaned out of temp to launch directory directory and temporary directory is removed at end of job
130. the gradient that is used to find the next IRC point is too small You can reduce the magnitude of the cutoff for determining when the gradient is too small with the keyword ircgcut which should be set Jaguar 7 0 User Manual 185 Chapter 8 The Jaguar Input File 186 to a value less than 1 0 If you set this keyword you should be careful not to set it so small that it does not filter out noise in the gradient The restart file for an IRC job includes the geometry of the last found IRC point This geom etry is in the zmat section An iremode downhill setting is included in the gen section regard less of the initial setting as a restart job proceeds downhill from the last found IRC point If the job has not proceeded far enough to have found another IRC point no iremode downhill setting is included 8 5 13 Solvation Keywords Most of the solvation keywords correspond to GUI options described in Section 3 9 on page 48 The allowed values for the solvation keywords are described in Table 8 24 Defaults for some of these keywords are not indicated in bold italics since the keywords default values generally depend on other keywords By default Jaguar calculations are performed in the gas phase so isolv 0 and all other solvation keywords are irrelevant The default values for the real valued parameters are for water The solvent can be specified with the solvent keyword instead of the dielectric constant and probe radius
131. the pseudospectral method itself Section 7 2 Section 7 3 and Section 7 4 describe GVBGVB RCI and LMP2 calculations and how the pseudospectral method improves computational scaling and efficiency for these methods Section 7 5 contains a brief description of density functional theory Chapter 3 includes information about performing Jaguar calculations using the techniques described here 7 1 The Pseudospectral Method Like conventional ab initio electronic structure codes Jaguar solves the Schr dinger equation iteratively using self consistent field methods to calculate the lowest energy wave function within the space spanned by the selected basis set For calculations on large molecules both conventional and pseudospectral techniques must recalculate key integral terms for each SCF iteration since storage costs for these terms are prohibitive Most of the fundamental integrals calculated in the pseudospectral method 1 9 are computed in physical space on a grid rather than in the spectral space defined by the basis functions The pseudospectral method takes the density matrix from the wave function at the beginning of each SCF iteration and the values of the integrals on the grid points and manipulates them to produce the necessary operators on the grid then assembles the Fock matrix by transforming these components back into spectral space where the Fock matrix is used in the usual way to generate the wave function for the next iteration
132. these libraries is included with the Jaguar distribution in the file SSCHRODINGER jaguar vversion lib Linux arch schrodinger mpi tar gz The library named libcmp so contains all of Jaguar s MPI functionality The other library libprun so contains code for constructing the mpirun launch command As Jaguar invokes mpirun automatically you should never invoke the jaguar launch script under mpirun The versions of these libraries that we provide in the Jaguar distribution are compiled to work with the MPICH 1 package from Argonne National Laboratory If you want to run Jaguar in parallel on computers with x86 processors and MPICH has already been installed and configured on them you can skip to Section 12 2 below but you may need to launch MPICH s secure servers first see Section 12 1 2 3 If you intend to run Jaguar in parallel using MPICH on an itanium2 1364 system that is not an SGI Altix system follow these instructions 1 Change to the SCHRODINGER jaguar vversion lib Linux ia64 directory 2 Make backup copies of the 1ibcmp so and libprun so libraries 3 Copy the four libraries in the disabled lib directory into the current directory cp disabled lib Linux ia64 so The versions of the 1ibcmp so and l1ibprun so libraries that you have just copied into the lib directory are compatible with MPICH 1 The two dummy libraries 1ibmpi so and libsdsm so are required to satisfy the dynamic library dependencies of the executabl
133. to all jobs described below them unless a later line of the same type replaces them Any OUTDIR TEMP Jaguar 7 0 User Manual Chapter 10 Running Jobs EXEC or FLAGS directive replaces any earlier setting made by the same directive and any of these settings can be reset to their default values with the value NONE for instance FLAGS NONE An OPTIONS directive clears all previously set options and creates a new options list An OPTIONS directive adds new options to the options list or redefines options already in the options list The syntax for the options set by OPTIONS directives is described later and summarized in Table 10 5 Table 10 4 Batch input file directives Directive Action EXEC directory OUTDIR directory SCRATCH directory TMPDIR directory WORKDIR directory files FLAGS options OPTIONS options OUTFILES files STRUCTOUT file IGNORE_ERRORS PURGE_JOBDB EXIT Set the directory for the Jaguar executable This directory can be any directory listed by jaguar LIST Set the directory to which output from jobs will be written The default is the job submission directory This directory is created auto matically if it does not exist Set the scratch directory Equivalent to specifying the JAGUAR_SCRATCH environment variable Set the scratch directory root Equivalent of tmpdir setting in schrodinger hosts Create the specified directo
134. use ip100 instead In canon ical orbital space the atom and function type labels are meaningless If a keyword is set to 4 5 9 or 10 the orbitals can be used for input in the guess section or for GAUSSIAN guess cards When the orbital output is in table form each function s coefficient for each orbital is shown with the functions shown in numbered rows and the orbitals in numbered columns When it is in list form each orbital is listed in turn with the function coefficients listed in order When ipx 2 n only coefficients larger than a particular value generally 05 are listed and the atom identifiers for instance h2 and function types for instance S for s Z for p are shown When ipx 4 n or ipx 5 n all coefficients are listed in order but without numbering Jaguar 7 0 User Manual 209 Chapter 8 The Jaguar Input File 210 For examples of the output that shows up in the output file for a calculation of water with a 6 31G basis set for various values of ip104 see the five examples given at the end of Section 5 6 on page 125 The five examples correspond to ip104 2 ip104 3 ip104 4 ip104 5 and ip104 6 in that order Only the first two occupied orbitals are shown in each case and not all functions are shown those gaps are indicated by 8 5 25 Grid and Dealiasing Function Keywords The grid and dealiasing function keywords allow the user to select from among the various sets of grids and dea
135. v eS Eae Le change Correlation tronic energy 41 210 305 94 44429831554 59822151704 73 87 14 44795282303 00970000923 137 2 63186441281 89225113857 78785135039 89560021182 15392320150 E I A F I H Just as for the gas phase SCF calculation the program scf lists energetic results for each iter ation of the solution phase calculation Then the various components A M of the solu tion phase energy or free energy are given These terms have the same meaning as for the converged gas phase wave function except the values listed in this table correspond to the converged solution phase wave function In particular the quantity called electronic energy is not the sum of the internal electronic energy of the solute plus the polarization free energy it is only the former Similarly the polarization free energy is not included in the one electron elec tron nuclear energy Jaguar 7 0 User Manual 107 Chapter 5 Output 108 Immediately following this output the various components of the solution phase free energy are printed out This output is given here Summary of solvation calculation by SM6 solvent water 0 E EN g gas phase elect nuc energy 95 816407393 a u 1 E EN liq elec nuc energy of solute 95 816088410 a u 2 G P liq polarization free energy of solvation 3 787 kcal mol 3 G ENP liq elect nuc pol free energy of system 95 822122793 a u
136. which treats bonds as having equal amounts of covalent and ionic char acter allows GVB to describe charge transfer reactions and bond breaking and formation accu rately and also gives better results for other molecular properties than an HF treatment alone can provide Jaguar 7 0 User Manual 143 Chapter 7 Theory 144 The goal of a GVB calculation then is to obtain pairs of GVB orbitals y and Wa where p ranges from 1 to the number of GVB pairs N that lead to a minimum energy for the molec gvb ular wave function N ovb Y II V 54V po V ppV pa CB Boo 4 p l For a given p the orbitals y and y form a pair that describes a particular bond or other pair of electrons Under the perfect pairing restriction the GVB orbitals within a pair are not orthogonal although they are each orthogonal to all GVB orbitals in other pairs For computa tional purposes it is useful to form orthogonal GVB natural orbitals y and y from the GVB orbitals y and y and their overlap S as follows Wat V pp Spe E 5 Vos 7 Si Em Fa V pa 7 V pb 5b Te P 8 The y orbitals generally have bonding character while the y orbitals are anti bonding The contribution to the GVB wave function from each pair is given by CoeW re pg CpuY pu py OB Boo 6 where the GVB configuration interaction CI coefficients C and C satisfy the following equations PE Pp 7a C 1 8 2 2r re
137. would result from the fitted charges and comparing it to the actual field If electrostatic potential fitting to atomic centers and bond midpoints is performed the bond midpoints are treated as dummy atoms and their descriptions and coordinates are provided before the grid points information The bond charges from the fit are provided with the label bond along with those on the atomic centers An example for water follows dummy atom x4 is between 2 and 1 dummy atom x5 is between 3 and d angstroms atom x y Z 0 0 0000000000 0 1135016000 0 0000000000 H1 0 7531080000 0 4540064000 0 0000000000 H2 0 7531080000 0 4540064000 0 0000000000 x4 0 3765540000 0 1702524000 0 0000000000 x5 0 3765540000 0 1702524000 0 0000000000 gridpoints used for charge fit 4162 out of a possible maximum of 4188 Electrostatic potential fitting constrained to reproduce total charge yes dipole moment no traceless quadrupole moment no traceless octupole moment no Atomic charges from electrostatic potential Atom 0 H1 H2 x4 x5 Charge 0 31208 0 63681 0 63681 0 48077 0 48077 Jaguar 7 0 User Manual Chapter 5 Output sum of atomic charges 0 000000 RMS Error 8 26E 04 hartrees If the fit is constrained to reproduce the dipole moment or dipole and higher moments or any other time both electrostatic potential fitting and multipole moment calculations are performed new moments can be calculated from the fitted charges a
138. you want only an optimized structure in solution and do not care about the computed solvation free energy you can skip the gas phase geometry optimization by selecting Input structure or Value under Gas phase reference energy These options allow you to use a reference energy other than that of the optimized gas phase structure 3 9 2 Solvation Model 6 Jaguar can treat solvated molecular systems using the SM6 model 157 In an SM6 calcula tion Jaguar first performs a gas phase energy calculation The polarization free energy of the system is computed in another SCF calculation with a reaction field based on the Generalized Born approximation 158 160 The partial atomic charges needed for this calculation are obtained from Charge Model 4 CM4 157 and the derivatives of the polarization free energy with respect to the electron density are determined analytically 161 The cost of carrying out a solution phase SCRF calculation with SM6 is roughly the same as that of a gas phase SCF calculation The SM6 solvation free energy is a sum of two terms the electronic nuclear polarization ENP term from the SCRF calculation and a cavity dispersion solvent structure CDS term The former ENP accounts for bulk electrostatic effects and the latter CDS accounts for first solvation shell effects 162 163 The solvation free energy is computed by adding to the free energy difference between the converged solution phase wave function and the co
139. 0 The Vibration panel The job should take only a few seconds even for a large molecule When the job finishes a new entry is added to the Project Table that includes a V button in the Vib column with which you can open the Vibration panel You can also generate a Molden input file after a frequency calculation enabling you to visu alize the frequencies with this program See Section 8 5 22 on page 206 for more information on writing a Molden input file 3 11 5 Infrared Intensities Infrared intensities can be computed analytically for closed shell HF wave functions in which the basis set does not have any effective core potentials or numerically for HF GVB or DFT wave functions To calculate infrared intensities for each frequency in km mol select IR Inten sities For closed shell HF calculations of IR intensities molecular symmetry is not used For calculations for which frequencies are computed numerically the numerical derivative of the dipole moment is used for IR intensity calculations Analytic IR intensities are only available with closed shell HF calculations If you want IR intensities for molecules in which the frequencies would normally be calculated analytically the frequencies must be computed numerically by setting nmder 2 in the gen section 3 11 6 Thermochemical Properties Thermochemistry calculations of the constant volume heat capacity C internal energy U entropy S enthalpy H and Gibbs free energ
140. 0 30 1529 51 1563 02 Thermodynamic properties calculated assuming an ideal gas In the table below the units for temperature are kelvins the units for U H and G are kcal mol and the units for Cv and S are cal mol K The zero point energy ZPE 6 670 kcal mol is not included in U H or G in the table below qa 298 15 K U Cv S H G trans 889 2 981 38 655 1 481 10 044 rot 889 2 981 23 636 889 6 158 vib 558 4 662 2 907 558 309 elec 000 000 000 000 000 total 2 335 10 623 65 198 2 928 16 511 Total internal energy Utot SCFE ZPE U 348 203415 hartrees Total enthalpy H Utot pV 348 202471 hartrees Total Gibbs free energy H T S 348 233448 hartrees end of program freq If infrared intensities were calculated several additional programs are run after the first run of the program scf These programs compute the derivatives of the dipole moment which are needed to calculate the IR intensities The IR intensities are listed in the frequencies table described above 5 3 9 CIS Calculations Output from CIS calculations of excited states lists the selected excited states with the excita tion energy from the ground state in eV and the transition wavelength the orbital excitations involved in the CI wave function and the transition dipole moment and oscillator strength The following example is for H O Excited State 1 9 3904 eV 132 03 nm Jaguar 7 0 User Manual Chapter 5 Output orbitals in excit
141. 1 You should not use the atom related options with any of the options that request information pertaining to the entire molecule the energy option for instance 5 2 Output From a Standard HF Calculation The contents of a Jaguar output file vary according to the calculation and output selections made This section describes the output file for a standard default single point closed shell Hartree Fock calculation Section 5 3 on page 96 describes the variations in the output file for the calculation options described in Chapter 3 All output files begin with a line listing the job name the machine upon which the job ran and the time the job was started followed by the general copyright information for the version of Jaguar which was used for the run The rest of this section describes output from each indi vidual Jaguar program run for a default calculation The output from the program pre begins with a description of the calculation to be performed the job name the directory containing the executables used to run the job the directory for temporary files comments from the input file if any and the names and paths of any non default data files used for the calculation see Section 8 1 on page 155 and Chapter 9 Next the basis set used for the calculation the molecule s net charge and multiplicity and the number of basis functions used for the calculation are specified This information is followed by the molecular geometry inpu
142. 14 31 Schlegel H B J Comput Chem 1982 3 214 Powell M J D Math Prog 1971 1 26 Bofill J M J Comp Chem 1994 15 1 Murtagh B A Sargent R W H Comp J 1970 13 185 Fletcher R In Practical Methods of Optimization Wiley New York 1987 Banerjee A Adams N Simons J Shepard R J Phys Chem 1985 89 52 Culot P Dive G Nguyen V H Ghuysen J M Theor Chim Acta 1992 82 189 Simons J Jorgensen P Taylor H Ozment J J Phys Chem 1983 87 27745 H ser M Ahlrichs R J Comput Chem 1989 10 104 Cremer D Gauss J J Comput Chem 1986 7 274 Alml f J Faegri K Ir Korsell K J Comput Chem 1982 3 385 Jaguar 7 0 User Manual References 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 Rabuck A D Scuseria G E J Chem Phys 1999 110 695 Bayly C I Cieplak P Cornell W D Kollman P A J Phys Chem 1993 97 10269 Stroud A H Approximate Calculation of Multiple Integrals Prentice Hall New York 1971 Lebedev V I Zh vychisl Mat mat Fiz 1975 15 48 54 Lebedev V I Zh vychisl Mat mat Fiz 1976 16 293 306 Lebedev V I Sibirsk Mat Zh 1977 18 132 142 Lebedev V I In Theory of Cubature Formula and Numerical Mathematics in Russian Sobolev S L Ed Nauka Sibirsk Otdel Novosibirsk 1980 pp 110 114 Cramer
143. 15051 1 000000 0 415051 H1 4 S 17 0 161278 0 181381 1 000000 0 181381 H1 5 X 18 1 100000 1 605761 1 000000 1 605761 Y 19 L 000000 1 605761 Z 20 L 000000 1 605761 H2 1 S 21 18 731137 0 214935 1 000000 0 214935 H2 2 S 21 2 825394 0 364571 1 000000 0 364571 H2 3 S 21 0 640122 0 415051 1 000000 0 415051 H2 4 S 22 0 161278 0 181381 1 000000 0 181381 H2 Be X 23 1 100000 1 605761 1 000000 1 605761 Y 24 L 000000 1 605761 Z 25 1 000000 1 605761 The table is followed by a list indicating the number of electrons in each atom that are treated with an effective core potential 5 3 11 Methods If the DIIS convergence method is not used the maximum DIIS error column is not printed for the table giving data from the SCF iterations Also if the OCBSE convergence scheme is selected the Coulomb and exchange contributions to the total two electron terms are listed in the SCF summary below the table If a fully analytic calculation is performed see Section 3 2 on page 30 the programs grid and rwr are not run because the all analytic method does not use this code If you select a Final localization method the output from the program local appears after the output from any SCF iterations and lists the orbitals that are localized If you want to print out the localized orbitals you should make the appropriate selection in the Output tab as described in Section 5 6 on page 125 Jaguar 7 0 User Manual Chapter 5 Output 5 4 Options for
144. 2 WWW http www schrodinger com FTP ftp ftp schrodinger com Generally e mail correspondence is best because you can send machine output if necessary When sending e mail messages please include the following information All relevant user input and machine output Jaguar purchaser company research institution or individual Primary Jaguar user Computer platform type Operating system with version number Jaguar version number Maestro version number mmshare version number On UNIX you can obtain much of the machine and system information listed above by entering the following command at a shell prompt SSCHRODINGER machid On Windows information is stored in the file schrodinger machid txt on your desktop If you have installed versions for more than one release there will be multiple copies of this file named schrodinger machid N txt where N is a number In this case you should check that you send the correct version of the file which will usually be the latest version If Maestro fails you can copy the information from the DOS window from which Maestro was launched To do so use the window manager menu in the top left corner of the window point to Edit then Select All and press ENTER The text is now in the buffer and can be pasted into a message Jaguar 7 0 User Manual References The first 18 references listed below provide general information about the algorithms used in Jaguar an
145. 2 Eg lvalerit SIGS 63 nui oon iu Oe kena Blk BER ee Mesi tel weet 308 13 2 3 Multiple Protonation Sites oiii trii teia ce eit edd 309 13 3 Training Set Hesulls 5 eee tet ane risa De ERR RU IA PATERE uEbca ne RR AGE 309 13 4 Running pK Calculations sss 311 13 4 1 Activating the pK Module niinc ntee 311 13 4 2 Running pK Calculations from Maestro 311 13 4 3 Jaguar Input Files for pK Calculations itio 2313 13 4 4 Running pK Calculations from the Command Line essesss 314 13 4 5 Monitoring pK Calculations eene ennemis 315 13 4 6 Choice of Initial Geometry eese 317 13 4 7 Recalculating pKa Values with New Parameters A 317 13 5 Developing Your Own pK Correction Parameters AA 318 STG Nl NR EO NT m 321 Li pie MINNS 323 leie E 333 Ke WOO IGS EE 347 Jaguar 7 0 User Manual xi xii Jaguar 7 0 User Manual Document Conventions In addition to the use of italics for names of documents the font conventions that are used in this document are summarized in the table below Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons and labels Monospace SSCHRODINGER maestro File names directory names commands envi ronment variables and screen output Italic filename Text that the user must replace with a value Sans serif CTRL H Keyboard keys upperc
146. 24 on page 207 and use the resulting output file s orbital output in the guess section of the input file for the next run A sample guess section for water with an STO 3G basis set follows The oxygen is atom 1 and for each molecular orbital coefficients for the oxygen s Is 2s 2p 2p and 2p orbitals are input The 1s coefficient for the first hydrogen atom follows followed by the 1s coefficient for the second hydrogen amp guess basgss sto 3g 1 orbital energy 20251577D 02 99421641D 00 25847131D 01 31906711D 02 88241647D 15 26760209D 02 55838749D 02 55838749D 02 2 orbital energy 12575489D 01 23376569D 00 84444935D 00 94117884D 01 39742456D 17 78936818D 01 15559441D 00 15559441D 00 3 orbital energy 59385470D 00 30846088D 09 13714419D 08 39372414D 00 21348436D 14 46944485D 00 44922200D 00 44922200D 00 4 orbital energy 45973017D 00 10403593D 00 53816730D 00 57914834D 00 40089482D 14 48573263D 00 29510298D 00 29510298D 00 5 orbital energy 39261707D 00 26538042D 15 27636653D 14 26424743D 14 10000000D 01 56164871D 15 78183836D 15 26536093D 14 8 11 The pointch Section The pointch section describes the locations and magnitudes of a set of point charges Up to 200 000 point charges may be used Each line of the pointch section should contain four real numbers the first specifying the point charge in atomic units and the next three spec
147. 321 program order specifying 233 235 programs included in Jaguar 233 properties ESP charge fitting ss 52 54 IN EEN 62 keywords sese 187 190 Mulliken population analysis 54 multipole moments ied NMR shielding constants nd jefe 52 63 UDP UE ccce rte p Hte 109 114 polarizability and hyperpolarizability 55 57 thermochemical sss 62 63 Properties tab cette 53 56 59 64 pseudospectral method 141 143 Python SCDE initis 279 Q QST guided transition state searches 75 additional structures for keyword LMP2 delocalization for quadratic energy error output keyword 205 quadratic synchronous transit see QST guided transition state searches quitting Maestro 3 R radian units for geometry input 164 radius COValent i cuente eet 222 yan der Waalsin 221 RCI restricted configuration interaction calculations 147 149 217 TAI ET 233 reactant geometry for IRC caleulapons 86 in transition state search 75 specifying in input file s 1239 specifying in Maestro 76 reading input files troubleshooting 288 redundant internal coordinates 70 keyword
148. 3P H Ar LACV3P K Cu Rb Ag H Ar 6 311G Zn Kr x H Ar 112 Cs La Hf Au Cd Xe Hg Bi LAV3P H Ar plus metal dif fuse d cc pVTZ pp Ga Kr In Xe H Ar Ca cc pVTZ 113 115 cc pVTZ pp f Ga Kr In Xe H Ar Ca cc pVTZ f 113 115 CSDZ Ce Lu H Ar 6 31G Zn Kr x H Ar 116 Cd Xe Hg Bi LAV3P H Ar K Cu Rb Ag Cs La Hf Au LACVP ERMLER2 K Lr H Ar 6 31G o H Ar 117 124 Ga Kr In Xe TI Rn The ECP basis set developed by Ermler and coworkers 117 122 named ERMLER2 is also available The basis set provided is the small core set that includes the outer core orbitals in the valence space in the same way as the LACV basis sets The basis set is a double zeta contraction in which the outermost primitive function in each symmetry has been uncon tracted The core is treated by a relativistic effective core potential for all elements For TI Rn the refitted ECPs have been taken from Wildman et al 123 but the basis set from the original ECPs has been retained because the new basis sets are much larger and do not match the basis sets for the other elements Polarization and diffuse functions for the 4p 5p and 6p elements have been added from the relativistic all electron double zeta set of Dyall 124 Jaguar 7 0 User Manual Chapter 3 Options In Table 3 2 the atoms described by the effective core potential are listed first followed by the atoms described by the alternat
149. 4 freezing for geometry optimization 14 71 72 160 TW EE EE 11 output keyword esee 205 bonding types describing in lewis files 255 bonds specifying for internal coordinates 163 Boys localization eene 48 Lee EEN 168 200 orbital printing 120 125 200 209 Output TON ia aero reet denn 120 C canonical orbital space output in 208 Cartesian coordinates format for geometry 10 11 158 freezing for geometry optimization 11 71 72 Ghi program DP eee rn erre tete 233 output from s 102 103 106 114 charge fitting see ESP fitting Mulliken population analysis charge molecular key words iens 164 setting in Maestro 18 charges atomic OMIA 57 from ESP fit ntc et enn 52 keyword for formal 220 Mullik n nnne eere 54 chemical shifts eesssssssss 57 190 CIS calculations 40 176 CiS EE 234 command options jaguar Fun 267 comment lines batcli seript sir ttes 272 input file configuration interaction CI Cl singles calculations 40 176 energy lowering for GVB pair natural OIDit ls iere terrere 99 GVB RCI theory eee 147 connectivity keyword for bonding 164 output keyword essen 205 output option 123
150. 45 0 edited nies 196 i E 177 MOPED P M 227 idelfrag oie en amens 227 TT incepet er ees 168 Idenavg cec eene nen 176 196 idfgrdX s3ss83s 139 198 e 220 EP 199 231 ee 167 168 Jaguar 7 0 User Manual 347 Keyword Index 348 180 228 M 161 178 mies 206 I V SNNT 207 ecl M 185 EIERE iore atest 185 Jaguar 7 0 User Manual de EE 185 le Or noise dte eee itis erieess 185 le E 185 istavg isurf J EE i TE E 169 175 JEsep odor etae ttai 195 K kesep ih nd rtt 187 204 L E ee 196 Iri 212 ldens 5e mentir 189 190 fr EEEN 188 Aa EEN 166 168 E EEN 166 187 262 Ur tre 168 locImp2yv iet reet 168 locposte eterne 200 lOCPOStV ener emet 200 Keyword Index UI EE 212 nu md 54 eesmosuno ner 32 192 193 M P DIL c 221 UE Nr eoe ttes 178 180 MASSIV co coda lt PR rtt 165 plotmi enee Eege 216 MAX TE 177 PIOWES ccc cac porre tret 216 maxdlis 5 cete repete CO ERE 193 195 Ji EE 191 Q QStUni eani Pe tede 179 R TU EE 189 CL UE 187 KE 195 e OT 191 S N SCA aane REOR 191 SCAMBUCSS 183 MUD CMA c 213 DER 183 nboden nbuck ncanorb le CO e X uoce tpe ll Ce e
151. 49 152 SettIngs ii asina ora epe ders 40 42 LMP pairs delocalization of 168 218 input file section for 168 218 keywords ntt 167 168 Imp2 program E lmp2der program 1mp2dip program 1mp2gda program 1mp2gdb program Jaguar 7 0 User Manual Output roii mioarei pre de oed 100 Local Density Approximation LDA 34 153 dftname values for sess 169 local job directory ssse 23 27 local LMP2 method 42 DTI St ese eue ed rtis 211 keywWotds ccr repeto o een tetro 205 local MP2 method see LMP2 method local LMP2 method Local program rete 234 localization of orbitals GVB LMP2 calculations 44 keywords ierece ett rnit 168 200 LMP calculations 41 168 options for final retten 48 log file 128 129 batch JODs is peoien 27 in Monitor panel sees 24 L wdin population analysis AT M machid program sse 234 machines LINUX file 294 297 Maestro Monitor panel s es 5 24 problems starting sss 285 286 Eu LEE 2 makejbasis utility eee 241 masses for frequency calculations 59 keyword setting in atomic section Mayer bond orders
152. 5 and Section 2 4 6 Section 2 4 6 also includes a description of how to specify bond length or angle constraints on the Z matrix coordinates for geometry optimizations You can orient the molecule or system using a label on the same line as the zmat section label This orientation label should begin with the word orient which is followed by an option in the form ab ab a b or a b where a and b are each either x y or z for example amp zmat orient x y Jaguar places the first atom in the Z matrix at the origin the second along the a axis in the negative direction for a and the third atom in the ab plane in the quadrant deter mined by the positive or negative signs of a and b To perform counterpoise calculations you can specify counterpoise atoms which have the usual basis functions for that element but include no nuclei or electrons by placing an sign Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File after the atom labels For example to place sodium basis functions at the Cartesian coordinates 0 0 0 0 1 0 you could include the following line in a Cartesian input file Nal 0 0 0 0 1 0 You can also input counterpoise atoms for geometries in Z matrix format If you are optimizing a molecular structure to obtain a minimum or a transition state you might want to refine the Hessian used for the job See Section 4 3 on page 74 for information on the methods used for transition state optimizatio
153. 5 4 3 2 Specifying Structures for the Reaction esee 76 4 3 3 Searching Along a Particular Hessian Eigenvechor 77 4 3 4 Refinement of the Initial Hessian eeeeeeeeeeenenennene n 78 4 4 Geometry SCANS EE 80 4 4 1 Setting up Scans inMaeslro iore tet tta iter ER erede A erede ra 80 44 2 Setting up Input Files for Stans EE 82 4 4 3 Constraining Coordinates for Torsional Scans seesseseeseerrerrerrereernsrnernererne 83 AAA Biestahtiigj E 83 4 4 5 SCAM RESUNS Es 83 4 5 Intrinsic Reaction Coordinate Calculations eee 84 Jaguar 7 0 User Manual Contents vi Chapter b CBIDML ua iuntiin hush tention Cad Ca Ca ape tame tans waar 87 5 1 Summarizing Jaguar Results 87 5 1 1 Reporting Final Results From One or More Jobe AA 90 5 1 2 Reporting Intermediate Results esee 91 5 1 3 Reporting Results for Each Atom ececeenesseceeeseesessesnessaeeenseeeeseeeesneeeeeees 92 5 2 Output From a Standard HF Calculation sese 92 5 3 Output File Content for Various Calculation Types eeeeeeeeeeeee 96 5 9 1 DE censa Em aM PI PEIUS EIE 97 5 9 2 JE MBB aic rep sch ca Sm wee mau Md RID MEM MD I 97 E BOTE EAV EES 98 5 3 4 Geometry or Transition State Optimization esee 99 5 3 5 SOWANOM is se 5 3 5 1 Out
154. 7 acidic site designating for pK calculations 313 AIMPAC w n file keyword 207 all analytic calculation keyword 195 analytic gradient of energy 69 convergence Cer 69 keywords ettet 177 183 analytic integral corrections REY WOT HE 195 specifying in cutoff file 254 theory Eed 143 angles see bond angles antiferromagnetic systems 134 227 atom labels forniat sac iai ieee 10 11 158 In Output iae eene Fee ito eivai 92 orbital output eee 126 209 atomic charges see charges atomic atomic masses for frequency calculations 59 keyword esses setting in atomic section atomic properties setting in atomic espe M 219 227 atomic units see units atomig file defau lt uei ette coit 237 description and format 242 243 specifying in input file s ssseseseeeeeeeeee 155 atoms eet nri erdt one 15 222 pun B 13 B babel using to convert file formats 201 204 using to read input files basis file description and format specifying in input file basis functions contracted iiec ete 117 118 derivatives of list in output 205 file containing eee 237 241 for individual atoms 222 in counterpoise calculations 14 16 158 keyword for printing
155. 7 0 09 0 42 S H1 0 15 S H2 0 15 Es si For the Format option All elements as f10 5 labels in table T 2 3 eigenvalues 20 55513 1 34560 Pesci 10 S 0 99466 0 21055 20 S 0 02122 0 47102 s SO Z 0 00155 0 08586 60 S 0 00430 0 41777 Lee 16 H1 S 0 00000 0 14851 eee 21 H2 S 0 00000 0 14851 Essa 25 H2 Z 0 00025 0 01342 For the Format option All elements as 19 15 in list 1 Orbital Energy 20 555133 Occupation 1 000000 Symmetry A1 0 994661070265476 0 021223773328496 0 000000000000000 0 000000000000000 0 001550431863529 0 004301782758377 0 000000000000000 0 000000000000000 0 000190485390547 0 003952404680376 0 003763985866478 0 003807504316264 0 000000000000000 0 000000000000000 0 000000000000000 0 000004988565650 0 000343482092802 0 000000000000000 0 000372571507087 0 000252040203901 0 000004988565650 0 000343482092802 0 000000000000000 0 000372571507087 0 000252040203901 2 Orbital Energy 1 345597 Occupation 1 000000 Symmetry A1 0 210549363265932 0 471018758398392 0 000000000000000 0 000000000000000 0 085862488931510 0 417774726334513 0 000000000000000 0 000000000000000 0 031498167188452 0 001405346737926 0 006172871870042 0 008194082815896 0 000000000000000 0 000000000000000 0 000000000000000 0 148513692384474 0 013067257872503 0 000000000000000 0 022047889711935 0 013419565122871 0 148513692384474 0 013067257872503 0 000000000000000 0 022047889711935 0 013419565122871 d Jaguar 7 0 Us
156. 81266 0 444634542184440 0 154328967291452 0 535328142270350 0 444634542175373 0 154328967293323 0 535328142276839 0 444634542180763 SP 0 1 12 1 0 0 636289746900000 0 147860053300000 4 808867839999999E 02 KKKK 9 996722918659862E 02 0 155916274998087 0 399512826086407 0 607683718592546 0 700115468876179 0 391957393095192 9 1 2 Effective Core Potential Format Basis sets containing effective core potentials ECPs are described in a slightly more compli cated fashion First the string 1 ECP must appear between the 5D or 6D label and the BACKUP Jaguar 7 0 User Manual 239 Chapter 9 Other Jaguar Files 240 label This string indicates that the basis set description contains information about the effec tive core potential associated with the basis set As for the basis sets without effective core potentials each atom in the set is described in turn The description begins with the basis function which is in the same format as those described above After a line with two asterisks the effective core potential is described The first line in the effective core potential description contains the element symbol e g Na and two numbers The first number is the maximum angular momentum in the core and the second gives the number of electrons replaced by the effective core potential Next the infor mation for various angular projectors is listed The first set of information contains the local compo
157. A eu sjueuieje 19440 UE 404 ABiaua aay uoezuejod eui ejnduioo oj pesn s jeu snipes quio noo orsuujul eui si enjeA puooes eui pue ysgvg Bale eoeuns eIqisseooe jueA os eu einduioo oj pesn si snipes jueAjos eui uum Buoje Jey snipes SJEEM Ja UBA eui si en eA ISI eui P S SI SnID8 9IUIO e y 10J Sen eA OM BJBYM sjueuieje 104 suomejnojeo UOHeAJOS Oe 104 pesn suio4sDue ul ipe 2ouo y erg a GeL 225 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File 226 Table 8 46 Covalent Radii in angstroms used to evaluate levels of interaction such as bonds between atoms Generally Jaguar considers two atoms bonded if the distance between them is less than cov ac times the sum of their covalent radii where covfac is keyword with a default value of 1 2 These radius settings can be altered by making cov settings in the atomic section of an input file as described in Section 8 8 1 H 0 32 3 Lij4 Be 5 6 C7 NI 1 23 0 90 0 82 0 77 0 75 11 Na 12 Mg 13 Alj14 Si ll5 Pi 1 54 1 36 1 18 1 11 1 06 19 K20 Cal Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 3 2 03 1 74 1 44 1 32 122 1 18 1 17 1 17 1 16 1 15 1 17 1 25 126 122 120 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 5 2 16 1 91 1 62 1 45 1 34 1 30 127 1 25 1 25
158. Atomic electrostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability rj L Electrostatic potential charges ESP Fit ESP to Atom centers zi Constraints Total charge only zd Grid type w Spherical Rectangular spacing 0 75 eoni Job B3LYP 6 31G Single Point Energy Solvation Start Read Write Edit Reset Close Help Figure 3 7 The Properties tab showing controls for ESP charges For electrostatic potential fitting of an LMP2 wave function you should also compute a dipole moment for more accurate results since the charge fitting will then include a coupled perturbed Hartree Fock CPHF term as well You might also want to constrain the charge fitting to reproduce the dipole moment as described below Because the CPHF term is compu tationally expensive it is not included in LMP2 charge fitting by default The fit can be constrained to reproduce the dipole moment and other higher moments if spec ified exactly by choosing the combination of moments from the Constraints option menu For LMP2 wave functions only dipole moments are available Keep in mind that the more 77 Keyword incdip in the gen section Jaguar 7 0 User Manual 53 Chapter 3 Options 54 constraints you apply to electrostatic potential fitting the less accurately the charge fitting will describe the
159. BO Sections To request a Natural Bond Orbital NBO analysis at the end of the Jaguar job include an nbo section in your input file If the section is empty as it is here amp nbo amp a default NBO analysis is performed Options for NBO calculations that are specified in the NBO keylist can be included in the nbo section in the format required by the NBO program Likewise if you want to specify options for the SCORE CHOOSE or SNRTSTR keylists you should include them in core choose and nrtstr sections in the Jaguar input file The informa tion in all these sections is copied unchanged into NBO keylists of the same name and passed to the NBO program Jaguar s interface to NBO 5 0 does not support the SDEL keylist which Jaguar 7 0 User Manual 235 means that Natural Energy Decomposition Analysis NEDA is not supported The DELH keylist is also not supported If you sets nboden 1 and mp2 3 in the gen section the LMP2 density is used in the NBO analysis If nboden 0 or is not set at all the HF density is used NBO calculations require an SCF calculation to be performed first For more details on NBO input and output see the NBO 5 0 Manual or visit the NBO web site http www chem wisc edu nboS 1 Please see the notice regarding third party programs and third party Web sites on the copyright page at the front of this manual 236 Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files Jaguar needs certai
160. Burke K Ernzerhof M Phys Rev Lett 1996 77 3865 Phys Rev Lett Erratum 1997 78 1386 Adamo C Barone V J Chem Phys 1998 108 664 Lynch B J Fast P L Harris M Truhlar D G J Phys Chem A 2000 104 4811 Xu X Goddard W A II Proc Natl Acad Sci U S A 2004 101 2673 Zhao Y Truhlar D G J Phys Chem A 2005 109 5656 Zhao Y Schultz N E Truhlar D G J Chem Phys 2005 123 161103 Zhao Y Schultz N E Truhlar D G J Chem Theory Comput 2006 2 364 Zhao Y Truhlar D G J Chem Phys 2006 125 194101 Zhao Y Truhlar D G J Phys Chem A 2006 110 13126 Zhao Y Truhlar D G Theor Chem Acc 2006 in press Meller C Plesset M S Phys Rev 1934 46 618 S b S Pulay P Theor Chim Acta 1986 69 357 S b S Pulay P Ann Rev Phys Chem 1993 44 213 S b S Tong W Pulay P J Chem Phys 1993 98 2170 Foster J M Boys S F Rev Mod Phys 1960 32 300 Pipek J Mezey P G J Chem Phys 1989 90 4916 Harding L B Goddard W A III J Am Chem Soc 1975 97 6293 Carter E A Goddard W A IN J Chem Phys 1987 86 862 Fischer T H Alml f J J Phys Chem 1992 96 9768 Jaguar 7 0 User Manual References 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 Schlegel H B Theor Chim Acta 1984 66 333 CRC Handbook of Chemis
161. CF methods keywords 193 194 SCE PLO STAM EE 233 GVB calculations eese 99 output from 94 96 98 99 101 102 105 solvation calculations 102 SCF tab 1 46 accuracy level m convergence controls 47 localization of orbitals we 48 Schr dinger contact information 322 SCHRODINGER directory 283 284 schrodinger hosts file 23 24 265 288 289 Scratch CITECLOLY enssins 273 SCRF method see self consistent reaction field scripts Jaguar batch eet tee 212 a e ertet 279 search method transition state TS second derivative of energy keywords 180 191 Jaguar 7 0 User Manual secure servers MPICH uses 297 Select Batch Script panel 26 self consistent reaction field method for solvation calculations esseeeeeeeeeee 48 52 102 shared memory Linux parallel calculations 295 shells information in output 93 Simons method for trust radius adjustment key WOT 525 sacs letras alan eee di 181 singlet open shell keyword for 199 SMG DIOBTAIm lt 0cincescsccysssnesescssnesoasstseeacererescean 234 SOLS e me hene 234 Qutput from e erect 105 106 SOJY program euet eni e tienen 234 output POM isc riter ei
162. Coulomb field around the molecule The dipole moment from fitting charges only is generally very close to the quantum mechanical dipole moment as calculated from the wave function Constraining the charge fitting to reproduce the dipole moment is generally not a problem but you might obtain poor results if you constrain the fitting to reproduce higher multipole moments However this option is useful for cases such as molecules with no net charge or dipole moment If both electrostatic potential fitting and multipole moment calculations are performed the moments are also computed from the fitted charges for purposes of comparison The electrostatic potential is itself computed on a grid By default this grid has the same form as the other pseudospectral grids it is formed by merging sets of spherical shells whose grid points are centered on each nucleus The Spherical option is selected by default in the Grid type section An alternative is to use a regular lattice of grid points 71 by choosing Rectangular in the Grid type section You can then set the spacing in bohr between points in this lattice in the text box HI For either grid type points within the molecular van der Waals surface are discarded The van der Waals surface used for this purpose is constructed using DREIDING 72 van der Waals radii for hydrogen and for carbon through argon and universal force field 69 van der Waals radii for all other elements These radii are listed i
163. DINGER environment variable you can run Jaguar jobs using the command SSCHRODINGER jaguar It is usually more convenient to include the installation directory in your PATH or path environment variable so that you do not need to type SCHRODINGER To determine whether jaguar is in your path enter the command jaguar help If the output from this command is a description of how to use the jaguar command Jaguar is already in your path and you can skip the rest of this subsection Otherwise if the output was an error message like jaguar Command not found you can add the installation directory to your path as follows csh tcsh setenv PATH installation directory SPATH bash ksh export path installation directory path Jaguar 7 0 User Manual Chapter 11 Troubleshooting 11 1 3 Problems Starting Maestro If you have problems when you try to start Maestro they are likely to involve permissions needed to do things over a network Most of these problems never arise if the machines you are using are within a local network If you are using only local hosts and still have these prob lems you might ask your system manager for advice in addition to following the instructions given here If you get the message Error Can t Open display you are probably trying to start Maestro from a machine that is not acting as your X server and this machine does not know what your display is Before starting Maestro you can sp
164. Electronic Structure Calculations on Large Molecules Ann Rev Phys Chem 1991 42 341 Pollard W T Friesner R A Efficient Fock matrix diagonalization by a Krylov space method J Chem Phys 1993 99 6742 Muller R P Langlois J M Ringnalda M N Friesner R A Goddard WA III A generalized direct inversion in the iterative subspace approach for generalized valence bond wave functions J Chem Phys 1994 100 1226 Jaguar 7 0 User Manual 323 References 324 12 13 14 15 16 17 18 19 20 21 22 23 24 Murphy R B Friesner R A Ringnalda M N Goddard W A III Pseudospectral Contracted Configuration Interaction From a Generalized Valence Bond Reference J Chem Phys 1994 101 2986 Greeley B H Russo T V Mainz D T Friesner R A Langlois J M Goddard W A II Donnelly R E Jr Ringnalda M N New Pseudospectral Algorithms for Electronic Structure Calculations Length Scale Separation and Analytical Two Elec tron Integral Corrections J Chem Phys 1994 101 4028 Langlois J M Yamasaki T Muller R P Goddard W A Rule Based Trial wave functions for Generalized Valence Bond Theory J Phys Chem 1994 98 13498 Tannor D J Marten B Murphy R Friesner R A Sitkoff D Nicholls A Ring nalda M Goddard W A II Honig B Accurate First Principles Calculation of Molecular Charge Distributions
165. Hessian The scan follows the grad ient from the initial point Downhill mode is set automatically in the restart file for IRC jobs The default calculation generates 6 points in both forward toward the products and backward toward the reactants directions from the transition state at an interval of 0 1 in the reaction coordinate You can enter the number of points in the Number of IRC points text box and the step size in the IRC step size text box You can also limit the number of geometry optimiza tion steps at each point in the Maximum optimization steps per point text box This value over rides any value set in the Optimization tab Finally for an IRC calculation Use mass weighted coordinates must be selected For an MEP calculation this option must be deselected When the calculation is finished the structures at the IRC or MEP points are automatically incorporated as separate entries in the Project Table and the reaction coordinate is incorpo rated as a property You can then sort the entries based on this property and display them in sequence using the ePlayer For an example see Section 3 7 of the Jaguar Quick Start Guide 30 Keyword inhess 4 in the gen section 31 Keyword iremode in the gen section 32 Keyword iremode downhill in the gen section 33 Keyword iremax in the gen section 34 Keyword irestep in the gen section 35 Keyword iremxcyc in the gen section 36 Keyword irc 2 in the ge
166. Jaguar 7 0 User Manual O Schr dinger Press Copyright 2007 Schr dinger LLC All rights reserved CombiGlide Epik Glide Impact Jaguar Liaison LigPrep Maestro Phase Prime PrimeX QikProp QikFit QikSim QSite SiteMap and Strike are trademarks of Schr dinger LLC Schr dinger and MacroModel are registered trademarks of Schr dinger LLC MCPRO is a trademark of William L Jorgensen To the maximum extent permitted by applicable law this publication is provided as is without warranty of any kind This publication may contain trademarks of other companies Please note that any third party programs Third Party Programs or third party Web sites Linked Sites referred to in this document may be subject to third party license agreements and fees Schr dinger LLC and its affiliates have no responsibility or liability directly or indirectly for the Third Party Programs or for the Linked Sites or for any damage or loss alleged to be caused by or in connection with use of or reliance thereon Any warranties that we make regarding our own products and services do not apply to the Third Party Programs or Linked Sites or to the interaction between or interoperability of our products and services and the Third Party Programs Referrals and links to Third Party Programs and Linked Sites do not constitute an endorsement of such Third Party Programs or Linked Sites The Schr dinger software distribution includes t
167. Jaguar 7 0 User Manual 197 Chapter 8 The Jaguar Input File 198 8 5 18 Initial Guess Keywords Table 8 29 lists the keywords related to the initial guess and the meaning of the values each keyword can take on Most of the keyword values in Table 8 29 correspond to options described in Section 3 8 on page 45 Table 8 29 Initial guess keywords Keyword Value Description igonly 0 1 No effect Use initial guess or input wave function for any post SCF calculations skipping SCF step No J K or Fock matrices are created therefore properties that require any of these matrices cannot be calculated iguess 0 10 11 25 30 Generate initial guess by diagonalizing one electron Hamiltonian Read initial guess from guess section from input file or from guess file specified in WAVEFNFILE line iguess 1 automatically if input file contains non empty guess section Construct initial guess from orbitals that give best overlap with atomic orbitals in default atomig or other atomig file listed in input file obtained by SCF calculations on atoms note that if guess section exists this is not the default choice Construct initial guess from orbitals whose densities when summed best agree with the sum of the densities of the atomic orbitals in default atomig or other atomig file listed in input file obtained by SCF calculations on atoms For a system that contains transition metal atoms construct a high
168. Manual Chapter 2 Running Jaguar From Maestro Jaguar input file is named jobname in the output file is named jobname out and the log file is named jobname 10g where jobname is the text that appears in the Name text box The default execution host the machine that the job will run on is selected in the Host option menu This default is localhost which means the machine on which Maestro is running The host name is followed by the number of available processors in parentheses If Jaguar is installed on more than one machine at your site you can change the choice of execution host by selecting another host from the option menu The Scratch directory option menu displays the directory on the execution host that will be used during the calculation to store temporary files You should check that the directory already exists on the execution host If it does not exist you should create it You should not need to change any other settings Click the Start button to start the job After you start the job the Monitor panel is displayed This panel is automatically updated to show the progress of your job As each separate program in the Jaguar code finishes running its completion is noted in the log text area When the program scf is running the Monitor panel displays the energy and other data of each iteration See Section 5 7 on page 128 on the log file for more information on this data You can close the Monitor panel by clicking the Close
169. OE no earlier than 3 2 Be sure to check the README file in usr lpp ppe poe and the man page for details on POE If you use LoadLeveler it must be a version that is no earlier than 2 1 You may need to set an environment variable in order to use multiple processors for a job The variable to set depends on how your machine has been configured specifically whether you are running the Job Manager or not The Job Manager manages pools of nodes and assigns specific parallel jobs to specific nodes To test whether you are using the Job Manager type ps aux grep jmd If you see jmd processes listed you are running the Job Manager In this case you need to tell Job Manager the pool from which you want to have nodes assigned to you The command jm status P lists the available pools and their member nodes The environment variable that sets your job pool is called MP RMPOOL and it should be set to the appropriate pool number csh tcsh setenv MP_RMPOOL 1 sh ksh bash export MP_RMPOOL 1 If your machine does not use the Job Manager you can set the environment variable MP_HOSTFILE to the file that contains the host list If MP_HOSTFILE is not set then the host file is assumed to be called host list and to reside in the current directory see the poe man Jaguar 7 0 User Manual Chapter 12 Parallel Jaguar page The host file should contain the names of the nodes on which parallel jobs can be run The node name is listed once for each p
170. PLOT 0061 PLOT LYTT 6vcC OIS I I6FI IV 8I ID LIS 9I d STIS TI IV el SIN CL EN II Ic9 L 789 T 009 T 009 T 006 T OPO ELEI OTTI N Olja 60O HN LO 9d ed pI ISTI 0Sr T SH cC H I suonejnojeo UOl eAJOS 10 sjueuiuBisse snipel SJEBM JAP ueA uo uoieulojul 9J0ui 104 al ejep siwe jnejep eui pue 9 6 uoijeg e uooes ees sdnoJb jeuorounj US ui suloje 10 ripe1 sjsn pe Ayjeiauab 1enDer eouis S3124 pJoq ui umous ase Mojaq sen pBA snipes asoym swoje 10 paubisseas aq ued pey suome no e2 uoneA os 49d 10 suoJsDuy ul pey SIeeM JOP UBA rr 8 aqel Jaguar 7 0 User Manual 224 The Jaguar Input File Chapter 8 00c ODOC ODOT OOT COT DOT SST 99T PLT OOT 007Z ODT OOC OOC OOC OOC ooz ooz UY 981V 68 Od r m Cd C8 LL 18 5H OS hV 6ZL d 8L I LLISO oa SLIM FvL UL LUH CcL TI LS ea oc e OTC 861 90c OOT LIC ECT BST CLT EDT OO OO OO OOC OOC OOC OOC OOC OOC eX PSII ES L TSAS Ieius Ou 6v PO Sr 9V LEID ot SrA Flo EplOW CP QN IP JZ IA 6 S SC LE 6 I OFI E9T OOT OO C OOC OOT OOC OOC OOC TH OCH SEPS vt SV CC CID It UZ Om 6c IN 8c 0OO LTA 9c UN SCHO vC A ETL TEPS ICD OC M ol Iv SIJO LI S Old STS rvI IV I I9 LOT SST OCT 00 C 00T eSI 8N L 94a ed PI 00 c ale sepiueujue pue sepiuljoe y 10 sen BA OWES Y e1e snipe quio no2 IISULJU pue snipe sjeeA Aaf ue
171. Phys Chem A 1998 102 1412 Scott A P Radom L J Phys Chem 1996 100 16502 Hehre W J Stewart R E Pople J A J Chem Phys 1969 51 2657 Hehre W J Ditchfield R Stewart R E Pople J A J Chem Phys 1970 52 2769 Pietro W J Levi B A Hehre W J Stewart R F Inorg Chem 1980 19 2225 Pietro W J Blurock E S Hout R F Jr Hehre W J DeFrees D J Stewart R F Inorg Chem 1980 20 3650 Collins J B Schleyer P von R Binkley J S Pople J A J Chem Phys 1976 64 5142 Binkley J S Pople J A Hehre W J J Am Chem Soc 1980 102 939 Jaguar 7 0 User Manual 327 References 328 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 Gordon M S Binkley J S Pople J A Pietro WI Hehre W J J Am Chem Soc 1982 104 2797 Pietro W J Francl M M Hehre W J DeFrees D J Pople J A Binkley J S J Am Chem Soc 1982 104 5039 Pulay P Fogarasi G Pang F Boggs J E J Am Chem Soc 1979 101 2550 Dill J D Pople J A J Chem Phys 1975 62 2921 Ditchfield R Hehre W J Pople J A J Chem Phys 1971 54 724 Hehre W J Pople J A J Chem Phys 1972 56 4233 Binkley J S Pople J A J Chem Phys 1977 66 879 Hariharan P C Pople J A Theor Chim Acta 1973 28 213 Hehre W J Ditchfi
172. RF continuum treatment of solvation and empirical corrections to repair deficiencies in both the ab initio and continuum solvation models This combination leads to high accuracy for a wide range of organic compounds in conjunction with tractable computational requirements The user interface has been designed to avoid the necessity of running the many individual jobs required to assemble the various components of the calculation Schr dinger has optimized each of the components for the best tradeoffs of accuracy versus efficiency The empirical correction terms which have been developed for ionizable groups relevant to the chemical and pharmaceutical industries are specifically designed to work with the basis sets electron corre lation levels and solvation model of the ab initio methodology The transferability of the corrections has been tested by examining a sizeable set of test molecules Several features of the method distinguish it from purely empirical fragment based approaches which are complementary to the present product First we expect that the use of ab initio quantum chemistry rather than fragment table lookups and interpolation will lead to a substantially wider range of applicability as well as significantly higher precision when the compound in question is not a direct entry in the empirical table Second our methods allow for a reasonable treatment of conformational effects which are in general entirely missing from fragme
173. SSIAN input 6 1 Choosing an Initial Guess The speed of convergence and sometimes simply obtaining convergence depends critically on the initial guess In the development of Jaguar we have attempted to provide default initial guesses of high quality These defaults are described below However there are situations in which the default initial guess for the molecule of interest does not lead to convergence or does not lead to the correct state Some suggestions on how to obtain alternative initial guesses are provided in this section 6 1 1 Overview By default for non GVB calculations on simple closed shell systems with no transition metals Jaguar constructs the initial wave function from orbitals that give the best overlap with previ ously calculated orbitals from atomic calculations The algorithm used is described in Ref 14 This method compares well with the semi empirical schemes that other ab initio programs use to obtain initial guesses Other methods for the initial guess can be selected with the iguess keyword including diagonalizing the one electron Hamiltonian which is rarely the best guess and using a superposition of atomic densities which provides a similar quality initial guess to the default However in cases where the default guess does not lead to the desired result this guess could provide an alternative that does Jaguar also provides a unique initial guess feature to improve SCF convergence both HF and DFT fo
174. Semi Empirical file Spartan Molecular Mechanics file Sybyl Mol file Sybyl Mol file Conjure file UniChem XYZ file XYZ file XED file Jaguar 7 0 User Manual 271 Chapter 10 Running Jobs 272 Babel cannot read Maestro formatted files For conversions between Schr dinger file formats that are not recognized by Babel there is a file conversion utility jagconvert This utility reads and writes Jaguar input in and output out files and Maestro mae files The utility is located in SCHRODINGER utilities The command syntax is as follows jagconvert intype infile outtype outfile where intype is one of ijag ijin ijout imae or imultimae and outtype is one of ojin omae or omultimae The input file is assumed to be a Jaguar input file if no input type is explicitly given MacroModel files are read in using imae If you convert a file that contains multiple structures only the first structure in the file is converted to the new format 10 2 Running Multiple Jobs jaguar batch If you need to run series of Jaguar jobs frequently you can create batch scripts that define the jobs and run them using the jaguar batch command For instance you might want to study the dissociation of a bond by evaluating the molecule s energy at various appropriate bond lengths scan a potential energy surface or perform a Hartree Fock level geometry optimiza tion and then evaluate the energy of the new structure using LMP2 or
175. The lowest energy configurations are degenerate The MO numbers with occupied metal d orbitals are given in the table above Jaguar will use the first configuration but you can select a different state configuration number from the table above with the istate keyword Using state configuration 1 2 1 1 0 0 In this example Jaguar has found six possible occupations of the five metal d orbitals that have essentially the same energy The table shows which MO numbers correspond to the metal d orbitals 9 13 in this example the occupation numbers 0 1 or 2 electrons per orbital and the relative energy in hartrees The lowest energy is the reference energy and is always 0 0 The probe program which follows h ig and ensures orthogonalization has no significant output The output for the grid generation done by the program grid lists the number of grid points for each atom as well as the total number of grid points for each grid used in the application of the pseudospectral method If you would like more information about these grids see Section 9 4 on page 248 The rwr program which generates the Q operators needed for the pseudospectral method runs next but has no significant output An example of the output from the next program scf again for a water molecule is given here and is explained below start of program scf number of electrons 10 number of alpha electrons number of beta electrons 5 number of or
176. User Manual 331 References 332 167 168 169 170 171 172 173 174 175 176 177 178 179 Thompson J D Xidos J D Sonbuchner T M Cramer C J Truhlar D G PhysChemComm 2002 5 117 Mayer I Chem Phys Lett 1983 97 270 Mayer I Chem Phys Lett 1985 117 396 Mayer I Int J Quantum Chem 1986 29 73 Chasman D Beachy M D Wang L Friesner R A Parallel Pseudospectral Elec tronic Structure I Hartree Fock Calculations J Comput Chem 1998 19 1017 Beachy M D Chasman D Murphy R B Friesner R A Parallel Pseudospectral Electronic Structure II Localized Mgller Plesset Calculations J Comput Chem 1998 19 1030 Jang Y H Sowers L C Cagin T Goddard W A III J Phys Chem A 2001 105 274 Langlois J M Ph D Dissertation California Institute of Technology Pasadena CA 1994 Perez Jorda J M Becke A D San Fabian E J Chem Phys 1994 100 6520 Baker J Andzelm J Scheiner A Delley B J Chem Phys 1994 101 8894 Mura M E Knowles P J J Chem Phys 1996 104 9848 Gonzalez C Schlegel H B J Chem Phys 1989 90 2154 J Chem Phys 1990 94 5523 Klicic J J Friesner R A Liu S Y Guida W C J Phys Chem A 2002 106 1327 Jaguar 7 0 User Manual Index A accuracy level 45 68 Lee BEE 194 accurate energetics eeeeeeeeeeceeeeeeeeeteteeeeees 2
177. Workspace to define the coordinate The coordinate and its type are listed in the Constraints table If you choose Cartesian you can choose which combination of coordinates x y or z to freeze from the Constrain in option menu For protein dihedral angles you can also select one of the standard angles by clicking Select and selecting the desired angle When you define constraints in this way internal coordinates are added to a coord section with a sign to indicate that the coordinate is frozen and Cartesian coordinate constraints are added to the zmat section by adding a sign after the constrained coordinates This means that the zmat section must be in the right format for the constraint If you edit the input file to add constraints you can freeze a specific coordinate by adding a sign at the end of its value in your geometry input in either the zmat or the zvar section For example to fix the HOH bond angle of water at 106 0 you could use the folloving Z matrix O H1 o 0 9428 H2 0 0 9428 H1 106 04 If you performed a geometry optimization on this input geometry the bond angle would remain frozen at 106 while the bond lengths varied To freeze a variable during an optimization add a sign to the end of the variable setting In this example the C H bond is frozen at 1 09 A chbond 1 09 HCHang 109 47 You can also freeze a variable by adding a sign to the variable in the Z matrix or the Carte sia
178. X file listing the nodes you want to use and set the envi ronment variable SCHRODINGER NODEFILE to point to this file Create a local machines LINUX file listing the nodes you want to use and set the SCHRODINGER MPI FLAGS environment variable to machinefile filename The file name must be the full path to the file Use of the HOST option overrides the use of the environment variables If the local host is in the list of available nodes the controlling MPI process runs on the node from which you execute the jaguar run command otherwise it runs on the first node in the node list 12 1 2 5 Troubleshooting Parallel Job Problems You can pass debugging options to the mpirun command using the SCHRODINGER MPI FLAGS environment variable by setting this variable to the quoted list of mpirun options Following is a list of common error messages and what to do to resolve the problem e Ifthe jobname Log file contains the error message error while loading shared libraries libhdf5 so cannot open shared object file No such file or directory then SCHRODINGER is not set on at least one of the nodes The serv p4 process transports the environment variables including SCHRODINGER to all job nodes If serv p4 is not running on all of the hosts being used in the job or if it is using the wrong communica tion port which must match your MPI PASSPORT value or if MPI USEPASSPORT is not set or is misspelled then SCHRODINGER w
179. a Y or N indicating whether the Fock matrix was updated or not The Fock matrix is updated using the difference in density matrix between iterations to accumulate contributions The next entry indicates whether the DIIS convergence scheme was used for that iteration also with a Y or N The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices including the one calculated during that iteration DIIS which is enabled by default usually starts on the second iteration and is not used on the final iteration If the entry in this column reads A it indicates that DIIS was not used for that iteration but the density matrix was averaged The cutoff set for each iteration is indicated under the icut heading Cutoff sets are explained in the cutoff file description in Section 9 5 on page 252 Jaguar 7 0 User Manual Chapter 5 Output The grid column lists the grid used for that iteration which must be one of the grid types coarse signified by a C medium M fine F or ultrafine U See Section 8 5 25 on page 210 and Section 9 4 on page 248 for more information on grids and grid types The total energy for the molecule in Hartrees appears in the next column followed by the energy change which is the difference in energy from the previous iteration to the current one The RMS density change column provides the root mean square of the change in density ma
180. a Coulomb exchange mean field operator describing the effect of the non excited GVB pairs on the RCI pairs This treatment effectively reduces the two electron part of the Hamiltonian to the space of the RCI coordinates Even for cases with many RCI pairs the configurations are restricted to those with only a small number of excitations and use the mean field treatment for each configuration s calculation The RCI spatial states eo add an extra complication to the necessary evaluation of Coulomb and exchange matrix elements using the natural orbitals y and y For the GVB case it is sufficient to compute the following matrix elements corresponding to Equation 10b and Equation 10c JA uoo aer vewa 12 HE Ypg Vy KI uv uv awol kowo DA Wad Pig where the u and v can each be any natural orbital For the RCI pairs on the other hand all matrix elements of the form A cB 8 o Be vy vu v E Woe Val KE ayb pg p qg tq are needed where the o and p natural orbitals are from the same RCI pair p and may be the same natural orbital while the y and A natural orbitals are from the same RCI pair with index q The complicated part of the calculation of the Coulomb and exchange operators then is evaluating matrix elements in atomic orbital AO space and using the AO space matrix Jaguar 7 0 User Manual Chapter 7 Theory elements to produce the matrix elements in the natural orbital space
181. a molecule you might want to freeze certain coordinates or constrain them to be equal to each other Freezing coordinates reduces the number of free parameters in the optimization and may reduce the number of steps to convergence or allow 9 Keyword inhess 1 in the gen section 10 Keyword inhess 0 in the gen section 11 Keyword inhess 1 in the gen section 12 Keyword inhess 4 in the gen section 13 Keyword intopt 1 in the gen section 14 Keyword intopt 0 in the gen section 15 Keyword intopt 2 in the gen section Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans you to converge a difficult optimization in stages Constraining coordinates can be used to enforce symmetry in either Z matrix coordinates or Cartesian coordinates 4 2 4 Freezing Specific Coordinates To constrain specific coordinates to their original values during an optimization you can use the controls in the Add New Constraint section of the Optimization tab or you can edit the input file The Edit Job dialog box provides a convenient way of editing the input file Using the Add New Constraint section of the Optimization tab see Figure 4 1 on page 68 you can pick atoms in the Workspace to define the coordinates to freeze First choose the coordi nate type Angle Cartesian Dihedral or Distance from the Type option menu then choose Atoms or Bonds from the Pick option menu then pick the required number of atoms or bonds in the
182. a process that normally requires a four index transformation By using the pseudospectral method however Jaguar reduces the scaling of the evaluation of each Coulomb or exchange matrix operator in basis function space from M to N and solves for the necessary matrix elements with a two index transformation rather than an expensive four index transformation For simplicity this process is described for the Coulomb matrix elements only the equations for K are similar First the usual three center one electron inte grals Au are evaluated in spectral space see Equation 2 The Coulomb matrix elements Ja are then evaluated in physical space for all y corresponding to orbital products of each RCI pair Man line YpgYpu gt and YpuYpu using the equation Jg M Grape 15 kl These matrix elements are transformed into spectral space to form J P where i and j are basis function indices using the pseudospectral method in the usual manner described in Section 7 1 on page 141 Jia Gal Qi J a Rs 16 where Q is the pseudospectral least squares operator and R is the value of the basis function j at grid point g final two index transformation EE a ij is performed to obtain the matrix elements in the natural orbital basis When Jaguar has obtained all Coulomb and exchange operators it performs an iterative diago nalization of the Hamiltonian to obtain the RCI coefficients The Davidson method is used for this step
183. abel file format conversions Format Keyword File Type alc Alchemy file prep AMBER PREP file bs Ball and Stick file bef MSI BGF file car Biosym CAR file boog Boogie file caccrt Cacao Cartesian file cadpac Cambridge CADPAC file charmm CHARMnm file c3dl Chem3D Cartesian 1 file c3d2 Chem3D Cartesian 2 file cssr CSD CSSR file fdat CSD FDAT file gstat CSD GSTAT file dock Dock Database file dpdb Dock PDB file feat Feature file fract Free Form Fractional file gamout GAMESS Output file gzmat Gaussian Z Matrix file gauout Gaussian 92 Output file g94 Gaussian 94 Output file gr96A GROMOS96 A file gr96N GROMOS96 nm file hin Hyperchem HIN file sdf MDL Isis SDF file jagin Jaguar Input file jagout Jaguar Output file m3d M3D file 270 Jaguar 7 0 User Manual Chapter 10 Running Jobs Table 10 3 Input format keywords and file types for babel file format conversions Continued Format Keyword macmol macmod micro mm2in mmd2out mm3 mmads mdi molen mopcrt mopint mopout pemod pdb psin psout msf schakal shelx smiles spar semi spmm mol mol2 wiz unixyz XYZ xed File Type Mac Molecule file Macromodel file Micro World file MM2 Input file MM2 Output file MM3 file MMADS file MDL MOL file file MOLIN file Mopac Cartesian file Mopac Internal file Mopac Output file PC Model file PDB file PS GVB Input file PS GVB Output file Quanta MSF file Schakal file ShelX file SMILES file Spartan file Spartan
184. ace that you want to map the data to in the Surface Table panel and click Display Options In the Display Options dialog box select Map values from volume data and choose a volume from the list below For a tutorial guide to generating and displaying orbital surfaces see Section 3 4 of the Jaguar Quick Start Guide Surface Table DE Isovalue Area m benzene orb MO 20 0 209055 MO_20 0 050 53 688 x E benzene orb MO 21 E 0 209050 MO 21 0 050 149 220 benzene_orb MO 22 E 0 020561 M0 22 0 050 s57 721 zem 2 benzene_orb MO 23 E 0 020551 MO 23 0 050 54 625 N Import Duplicate Delete Limit Export to CNS Map Display Options 0 05 nm lsovalu 7 ji 0 05 0 00 Sigma Display at most Close Help Figure 3 12 The Surface Table panel Jaguar 7 0 User Manual 65 Surface Table Display Options Lol 0 Transparency 1 7 0 Style Solid w Mesh w Dot Color scheme wv Property Constant Color Red m Set Default Surface Color Negative color Blue z wv Map values from volume data pati OK Apply Cancel Help Figure 3 13 The Display Options dialog box 66 Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans For Hartree Fock GVB LMP2 and DFT calculations in gas phase or in solution Jaguar c
185. acted dealiasing func tions are simply formed by specifying the exponent of the Gaussian function Contracted dealiasing functions are defined as linear combinations of the appropriate type of functions the coefficients and exponents for the linear combination are the same as those used in the basis set for the contracted basis functions for the relevant function types 1s 2s 2p etc depending on the molecule and the basis set Thus a dealiasing uncontracted function can be specified by dictating the type s p d etc and the exponent desired for the Gaussian while a contracted Gaussian function can be specified by dictating the type and referencing which set of contrac tion coefficients and exponents are desired Section 9 3 1 below describes the file that determines the dealiasing functions for a calculation Sets of dealiasing functions must be provided for each grid used in the calculation Comments about a sample file refer to the sample dat file in Section 9 3 2 on page 246 9 3 1 File Format and Description The first line of a dealiasing function file contains a character string which includes the version number of Jaguar This string should be dafv followed immediately by four digits giving the version number times 100 Lead zeros are added if necessary The second line has two integers The first integer gives the number of dealiasing function sets provided for each atom type each set is used for a particular grid during
186. ained and the calculation might not converge Similarly the ordering of the basis functions within the set being used must be the same as that used for the ordering of coeffi cients in the guess section This next line of the section should begin with a set of coefficients describing the contribution of each function in the basis set to the first molecular orbital and continue on with similar coefficient sets for each molecular orbital A single line whose content is unimportant should precede each molecular orbital s set of coefficients If you like you can use this line to label the molecular orbital for your own convenience If you choose to write the occupied orbitals or occupied and virtual orbitals from one run and use them in the guess section for another run you must make sure to choose a proper format From the Orbitals window in the GUI you could select occupied orbitals or all orbitals from the What option menu and all elements as f19 15 in list or all elements as f8 5 in list from the How option menu for the original run as described in Section 5 6 on page 125 and the resulting orbital output could be copied from the output file into the guess section of the input file for the next run Similarly you could set the relevant orbital output keyword to 4 5 9 or 10 in the gen Jaguar 7 0 User Manual 229 Chapter 8 The Jaguar Input File 230 section of the input file for the first run as described in Section 8 5
187. air on atoms from the nitrogen group two for those from the oxygen group three for the fluorine group and one for the carbon group In the last case assigning lone pairs is only reasonable when the atom is bonded to only two neighbors If you assign one GVB lone pair for an atom you should also assign any other possible GVB lone pairs on that atom 6 5 Restarting Jobs and Using Previous Results Sometimes you may find it useful to restart a job either because you want to refine the results and do not want to start from the beginning of the calculation because you want to alter the calculation slightly but want to use an initial guess or geometry from the previous run or because you encountered some sort of problem that prevented the job from finishing New input files which are also called restart files generated during each job can be used to restart the jobs These files are automatically written to your local job directory at the end of a run if the run did not finish you can usually find the new input file by following the directions at the end of this section Jaguar 7 0 User Manual Chapter 6 Using Jaguar The restart file contains all the information needed for a new run incorporating the results from the first run This file contains the same job settings you made for the original input file for the job but also contains the results of the job the final wave function the final geometry and the like Thus if you want to
188. al Chapter 8 The Jaguar Input File Table 8 42 Keywords for physical properties in the atomic section Keyword Description isotope Isotopic number integer e g 2 for deuterium overridden by atom s mass setting if it exists mass Nuclear mass in amu esp Electrostatic potential fitted point charge or request to fit charge to dummy atom see text formal Formal charge integer value on atom multip Spin multiplicity of atom or fragment containing atom 2spin Number of unpaired alpha or beta electrons on atom positive value for alpha spin negative value for beta spin mulk Mulliken population vdw van der Waals radii in A for charge fitting vdw2 van der Waals radii in A for PBF solvation Not applicable to SM6 solvation cov Covalent radius in A used to determine bonding and other properties guess for transition metal containing systems along with the multip keyword See Section 6 1 3 on page 133 for more information on using this improved initial guess method The esp keyword can be used to freeze the charge on an atom to a particular value while fitting charges to other atoms leave an atom out of charge fitting or fit a charge to a dummy atom If the esp column entry for an atom is set to a real number the atomic charge for that atom will be held fixed to that number during charge fitting If the esp column entry for an atom is set to n or no or 0 the atom will not be included in charge fitting
189. al functional 34 Becke 1988 nonlocal gradient correction 37 correlation Vosko Wilk Nusair VWN local functional 35 Lee Yang Parr local and nonlocal functional 38 See refs 32 and 33 B3PW917 Exchange exact HF Slater local functional 34 Becke 1988 nonlocal gradi ent correction 37 correlation Perdew Wang 1991 local and GGA II nonlocal func tional 36 B3P86 Exchange exact HF Slater local exchange functional 34 Becke 1988 nonlo cal gradient correction 37 correlation Vosko Wilk Nusair VWN local functional 35 Perdew 1986 nonlocal gradient correction 40 B97 17 gt Reparametrization of Becke s 1997 hybrid functional 42 by Hamprecht Cohen Tozer and Handy 45 B98 Becke s 1998 hybrid functional including the Laplacian of the density and kinetic energy density terms as well as gradient terms 43 SB987 Schmider and Becke reparametrization of Becke s 1998 functional 44 BHandH 50 exact HF exchange 50 Slater local exchange functional 34 Keyword dftname pwpw91 in the gen section Keyword dftname pbe in the gen section Keyword dftname hcth407 in the gen section Keyword dftname m06 1 in the gen section Keyword dftname b3lyp in the gen section Keyword dftname b3pw91 in the gen section Keyword dftname b3p86 in the gen section Keyword dftname b97 1 in the gen section Keyword dftname b98 in the gen section Keyword dftname sb98 in the gen section Keyword dftn
190. aluating analytic gradients at 6N perturbed geometries unless the ato Jaguar 7 0 User Manual Chapter 5 Output number of perturbed geometries needed is reduced by the use of molecular symmetry After the calculations at the perturbed geometry Jaguar performs one final calculation at the unper turbed geometry The Jaguar programs run may vary slightly for non HF calculations as described earlier in this section After the data from all perturbed geometries is collected the program nude prints the numerical first derivatives in a force table similar to the usual geom etry optimization force table described earlier in this section The output then lists the matrix indices of the most asymmetrical Hessian element before symmetrization The symmetrized numerical Hessian is not printed in the output but can be found in the restart file which is discussed in Section 6 5 on page 136 For either analytic or numerical frequency calculations the output from the program freq contains the actual frequencies and normal modes from the computed Hessian or from the last available Hessian generally the initial Hessian guess if you used the Use available Hessian choice to request vibrational frequencies The output from the program freq first lists the harmonic frequencies in cm and their symmetries if symmetry is on for the job then the normal modes The system s thermochemical properties the constant volume heat capacity C en
191. alue 0 00 hartree Job BSLYP MIDIX Single Point Energy Solvation Start Read Write Edit Reset Close Help Figure 3 6 The Solvation tab These charges are passed to the Poisson Boltzmann solver which then determines the reaction field by numerical solution of the Poisson Boltzmann equations and represents the solvent as a layer of charges at the molecular surface which serves as a dielectric continuum boundary These solvent point charges are returned to Jaguar s SCF program which performs another quantum mechanical wave function calculation incorporating the solvent charges This process is repeated until self consistency is obtained The cost is roughly twice that of a gas phase calculation Solvation free energies can be computed with HF DFT GVB or LMP2 wave functions For GVB or local LMP2 solvation free energy calculations we recommend using heteroatom pairs Jaguar 7 0 User Manual 49 Chapter 3 Options 50 for the most efficient results particularly since solvation free energy calculations often use radii optimized for calculations that use heteroatom pairs See Section 9 6 on page 254 for more details see Section 3 5 on page 40 and Section 3 6 on page 43 for information on setting LMP2 or GVB pairs Solvent parameters are set in the Solvation tab To select the standard Poisson Boltzmann model choose PBF from the Solvent model option menu You can choose the solvent
192. ame bhandh in the gen section Jaguar 7 0 User Manual Chapter 3 Options BHandHLYP Exchange 50 exact HF exchange 50 Slater local exchange functional 34 correlation Lee Yang Parr local and nonlocal functionals 38 X3LYP Extension of B3LYP by Xu and Goddard to include Perdew Wang 1991 gradi ent correction exchange functional 36 with exchange parametrized to fit Gaussian exchange density 50 MPW1K Reoptimization of mPW1PW91 functional parameter for prediction of reac tion barrier heights by Lynch Fast Harris and Truhlar 49 MPW1PW91 Hybrid functional including modification of Perdew Wang gradient cor rection exchange functional by Adamo and Barone 48 Exchange Exact HF exchange Slater local functional 34 Perdew Wang 1991 gradient correction functional 36 cor relation Perdew Wang 1991 GGA II local and nonlocal functionals 36 PWB6K Reoptimization of MPWBIK functionals for simultaneous accuracy of bond energies barrier heights and nonbonded interactions by Zhao and Truhlar 51 PW6B95 Reoptimization of MPW1B95 functionals for simultaneous accuracy of bond energies barrier heights and nonbonded interactions by Zhao and Truhlar 51 Mo5 Hybrid functional parametrized for broad accuracy including noncovalent inter actions kinetics and interactions with metals by Zhao Schultz and Truhlar 52 53 MO05 2X Hybrid functional with larger HF exchange component similar
193. an use calculated analytic gradients to optimize the molecular geometry to a minimum energy structure or a transition state In addition to locating stationary points Jaguar can calculate points along one or more coordinates with or without optimizing the other coordinates These scans include intrinsic reaction coordinate IRC and minimum energy path MEP scans as well as geometry scans of specified coordinates There are five tasks on the Jaguar submenu of the Applications menu that support optimiza tions and scans Optimization Relaxed Coordinate Scan Rigid Coordinate Scan Transition State Search Reaction Coordinate Throughout this chapter footnotes indicate the Jaguar input file keywords and sections that correspond to particular GUI settings If you are working from the GUI you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the GUI or if you want to edit keywords directly by using the Edit Job window described in Section 2 3 on page 8 4 1 Geometry Optimization The Basics To perform a geometry optimization you need a guess at the geometry and the direction in which to search a set of coordinates to optimize and some criteria for when the optimization is complete The search direction is obtained from the gradient of the energy and the initial Hessian The general settings for geometry optimizations are in the Optimization tab of the Jaguar p
194. an set up input files for a range of Jaguar jobs and start the jobs To open the panel choose the task or calculation type from the Jaguar submenu of the Applications menu in the main window The available tasks are Single Point Energy Optimization Relaxed Coordinate Scan Rigid Coordinate Scan Transition State Search Reaction Coordinate Initial Guess Only Below these tasks in the menu are two calculation types that are run as Jaguar batch jobs pKa e J2 The input for these calculations is described in this chapter and Chapter 13 Most of the Jaguar panel is occupied by a set of tabs in which you can make settings for jobs These tabs are described in Chapter 3 At the top of the panel is a section for selecting the source of job input The Use structures from option menu has three choices e Workspace included entries the structures that are displayed in the Workspace e Selected entries the structures that are selected in the Project Table These need not be the same as the included entries Selected structure files the structures that are in the files listed in the Files text box You can navigate to the desired files using the Browse button When you click OK in the file selector that is displayed the file name is added to the list in the Files text box If you select either of the first two sources of job input the results of the calculations can be incorporated into the Maestro project If you
195. and or the number of all other bonds the atom has A bonding type group describes elements of bonded atoms and orders of those bonds as described in Section 9 6 1 The third integer in an atom type description line determines how many bonds the atom forms of each bonding type group g for an atom of a particular element where g indicates the order of the bonding type groups listed for that element The number of bonds from group g is indicated by the 10 digit in the integer For example if g were 1 and the atom being described were carbon g would correspond to the first bonding type group listed for carbon and a bonding type integer value of 40 4 x 10 would indicate that the carbon atom in question had four bonds from carbon s Group 1 bonding type information If the Lewis file contained the bonding type information example provided in Section 9 6 1 which included the lines 6 CARBON Group 1 C H bonds only Group must be here the rest is a comment Bond order 1 this should be a non blank comment line 1 element 1 the atomic number of H the integer value of 40 would describe a methane carbon The same sample Lewis file informa tion whose key Group 2 information for carbon appears in these lines Group 2 C C and C 0 bonds Bond order 1 0 elements Bond order 2 2 elements 6 8 Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files would mean that this radius information line 6 1 120 1 1 1 2 00 C in H2 C C or H2 C 0
196. and shared memory segments config Describe the MPICH configuration Jaguar 7 0 User Manual 297 Chapter 12 Parallel Jaguar 298 The secure server can also be launched manually on a single machine with the command MPICH_install bin serv_p4 o p port This is the command actually used by the mpich utility script described above Table 12 2 Options for the mpich script Option Meaning p port Specify the port number for servers The default port is 1234 m hostfile Specify a file listing the MPICH host machines The default file is machines LINUX h host list Act just on the specified hosts The default is to act on all hosts in the host file u user Connect to remote machines as the specified user v Report the version number of the mpich script d Provide debugging output While serv_p4 provides a fast secure method of transmitting the environment throughout a network it may not be compatible with certain security settings file system configurations or user authentication mechanisms If you believe that serv_p4 is incompatible with your computing environment you may be able to avoid using it by setting the environment variables that Jaguar needs in your shell startup scrips In addition to setting SCHRODINGER to the instal lation directory you must set the following environment variables JAGUAR_EXEC SCHRODINGER jaguar vjversion bin Linux arch MMSHARE_EXEC SCHRODINGER mmshare vmversion bin Linux arch
197. anel Figure 4 1 This tab is present for all of the tasks listed above except Rigid Coor dinate Scan for which no optimization takes place Four of the tasks have tabs in which settings are made that are specific to the task These tabs Transition State Scan and IRC are described in later sections 1 Keyword igeopt 1 in the gen section 2 Keyword igeopt 2 in the gen section 3 Keyword irc 1 in the gen section Jaguar 7 0 User Manual 67 Chapter 4 Optimizations and Scans 68 Jaguar jaguar a Use structures from Workspace included entries Molecule Theory scr Optimization Properties Solvation Output Maximum steps 100 Convergence criteria Default w Loose Initial Hessian Schlegel guess Coordinates Redundant internal Add new constraint Type Cartesian Constrain in XYZ 1 F Pick Atoms Seteei Constraints Constraint Type Selected constraint M C1 H4 Angle X1 Cartesian XYZ 0 0000 Constrain in XYZ 4 E Dynamic Target value Delete Delete All Start Read Write Edit Reset Close Help Figure 4 1 The Optimization tab 4 1 1 SCF and Geometry Convergence During geometry optimization Jaguar adjusts the convergence criteria for the SCF calculations at each geometry step for efficiency For the initial iterations of an optimization the SCF calcu lations are
198. anual Chapter 10 Running Jobs Table 10 6 The jaguar batch command line options Option Description C Create input files but don t run the batch job nolocal Do not run in the local directory r Restart option Skip execution of steps that are completed i e steps that have input files and completed output files The default action is to generate Jaguar input files from template files even if they overwrite previously existing files and run the corresponding job step 1 Lists jobs that would be run if jaguar batch were called without options but does not generate any files or run any jobs s Lists jobs that would be run and shows the contents of the input files that would be gen erated if jaguar batch were called without options but does not generate any files or run any jobs The r option is a restart option which prevents jaguar batch from overwriting existing Jaguar input and output files and from running the job steps that created them The 1 and s options permit you to see what jaguar batch would do but do not actually allow it to generate any new input files or run any Jaguar jobs The jaguar batch command accepts both Jaguar input files jobname in and Maestro files jobname mae as input and you can specify both on the same command line Maestro files are used as a source of structures only and jaguar batch creates a Jaguar input file for each structure in the Maestro file using the commands in the
199. ape to the actual solute molecule as described in reference 15 is included The last solution phase energy component shown only if it is nonzero is term T the first shell correction factor which depends on the func tional groups in the molecule with atoms near the surface contributing most heavily Finally the list ends with the reorganization energy and the solvation energy The reorganiza tion energy is the difference between the total solute energy and the gas phase energy and does not explicitly contain solvent terms The final solvation energy is calculated as the solution phase energy described above minus the gas phase energy The results of the self consistent reaction field iterations so far performed are summarized after the scf output in the output from the program sole An example from the final SCRF iteration of water in cyclohexane follows start of program sole SCRF solvation energy iteration Hartrees kcal mol 0 0 0000000 0 0000 d 0 0024304 1 5251 2 0 0027473 1 7240 3 0 0027918 1 7519 stopping solvation energy converged iterations 3 sfinal 1 7519 kcal mol end of program sole The solvation energy is listed in Hartrees and in kcal mol and the note below it reads either solvation energy not yet converged or stopping solvation energy converged depending on whether the solvation energy has changed by less than the Solvation Jaguar 7 0 User Manual 105 Chapter 5 Output 106 conver
200. ar orbital i on grid point g R is the physical space representation of virtual orbital p and A is the three center one electron inte gral over the occupied molecular orbital j and the local virtual orbital g The last term is related to the three center one electron integrals in atomic orbital space Au described in Equation 2 by due EEN 23 The summation is performed in two steps first summing over k to form intermediates A A jig 2 Ci Aug gt 24 then summing over to yield the integrals in molecular orbital space A igg 2A ite 25 Jaguar s local MP2 module also includes analytical corrections similar to those described earlier for Hartree Fock and GVB calculations and a length scales algorithm both of which are explained in reference 13 7 5 Density Functional Theory Density functional theory DFT is based on the Hohenberg Kohn theorem 131 which states that the exact energy of a system can be expressed as a functional depending only on the elec tron density In the Kohn Sham implementation of DFT 132 this density is expressed in terms of Kohn Sham orbitals y occ pa 2Y vio 26 similarly to the density expression used for Hartree Fock SCF calculations For simplicity we consider only closed shell systems in this overview of the method Jaguar 7 0 User Manual Chapter 7 Theory The Kohn Sham orbitals are expressed as a linear combination of basis functions 1 and the
201. are even tighter very accurate and only the ultrafine pseudospectral grid type is used The Ultrafine setting may be helpful for cases with convergence or accuracy problems but increases the computational cost by a factor of two to three The final choice is Fully analytic which turns off the pseudospectral method and uses the analytic methods for all integrals 126 127 This choice is significantly slower than the pseu dospectral method 3 8 2 Convergence Criteria SCF calculations finish when the calculations converge the maximum number of iterations is exceeded or Jaguar determines that the calculation cannot converge The maximum number of iterations and the convergence criteria are set in the Convergence criteria section You can set the maximum number of SCF iterations in the Maximum iterations text box Generally Hartree Fock calculations for simple organic molecules converge in fewer than 10 iterations while complex calculations using higher level methods or involving open shells can take a few extra iterations Molecules that include transition metals can converge more slowly 50 Keyword iacc 3 in the gen section 51 Keyword iacc 2 in the gen section 52 Keyword iacc 1 in the gen section 53 Keyword nops 1 in the gen section 54 Keyword maxit in the gen section Jaguar 7 0 User Manual 45 Chapter 3 Options 46 Jaguar jaguar a Use structures from Workspace included entries Molec
202. are the same as those of the actual solute molecule as described in reference 15 The output from the program solv follows the Poisson Boltzmann solver results giving the number of point charges provided by the solver to model the solvent the sum of the surface charges the nuclear repulsion energy already calculated by Jaguar the nuclear point charge energy representing the energy of interaction between the molecule s nuclei and the solvent point charges and the point charge repulsion energy which is calculated but not used by the rest of Jaguar because it is irrelevant to the desired solvation results After this output the output for the second solvation iteration begins The output from scf comes first giving the results for the molecule and solvent point charges system An example from the first solute with solvent point charges scf run in a calculation of 6 31G water in cyclohexane using the Jaguar solver is given here start of program scf i ud i g Jaguar 7 0 User Manual 103 Chapter 5 Output 104 LB cor RMS maximum e d i energy density DIIS r t ue ta total energy change change error etot 1 N N 2 U 76 03588607997 6 8E 04 6 6E 03 etot 2 YY 06 oM 76 03615425936 2 7E 04 1 9E 04 1 8E 03 etot 3 Y N 6M 76 03617415619 2 0E 05 0 0E 00 0 0E 00 Energy components in hartrees A Total zero electron terms 9 35161183359 B Nuclear nuclear 9 33000672144 C Nuclear sol
203. arget value c for an internal coordinate it must follow the radius a A target value cannot be specified for a Cartesian harmonic constraint The units of the force constant the half width and the target coordinate values are specified by the gen section keywords iunit and eunit The Cartesian position is specified by a single atom label as in the following example amp coord C1 hc 10 0 amp The following example specifies a harmonic constraint on a bond length with a force constant of 10 0 kcal mol AT a width of 0 1 A and a target bond length of 1 5 A amp coord C1 C2 he 10 0 0 1 1 5 amp In this constraining potential the bond length can vary freely between 1 4 and 1 6 but the energy rises if it goes outside this region 4 2 3 Applying Constraints by Using Variables When you define a set of coordinates bond lengths or bond angles in terms of a variable these coordinates bond lengths or bond angles are constrained to be the same during a geometry optimization The variable becomes the optimization parameter and the coordinates bond lengths or bond angles are set to the value of the variable at each optimization step The effect of using variables depends upon the format of your input structure If your input structure is in Z matrix format you can set several bond length or angle coordinates to the same variable For input in Cartesian format you can use variables to keep several atoms within the same pla
204. as a constraint also constraining to dipole moment if k 1 to quadrupole moment if j 1 and to octupole moment if i 1 1 Do all incdip options sequentially Idips Do not calculate any multipole moments Calculate dipole moments Calculate dipole and quadrupole moments Calculate dipole quadrupole and octupole moments nN d Ww N N Calculate dipole quadrupole octupole and hexadecapole moments Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 25 Keywords for charge fitting multipole moment and polarizability and hyperpolariz ability calculations Continued Keyword Value Description ipolar 0 Do not calculate polarizabilities or hyperpolarizabilities 2 Calculate polarizabilities o and first and second hyperpolarizabilities B and y using CPHF method 1 Calculate polarizabilities and hyperpolarizabilities B using CPHF method 1 Calculate polarizabilities using 3 point finite field method 2 Calculate polarizabilities and hyperpolarizabilities using 3 point finite field method 5 Calculate polarizabilities and hyperpolarizabilities using 5 point finite field method 7 Calculate polarizabilities and hyperpolarizabilities using 7 point finite field method efield 0 024 Electric field for polarizability and hyperpolarizability calculations in au default is 0 006 for ipolar 1 Idens 0 Do not calculate electron density 1 Calculate electron density on grid grid choice set by grid keyword geldens ultraf
205. ase In descriptions of command syntax the following UNIX conventions are used braces enclose a choice of required items square brackets enclose optional items and the bar symbol separates items in a list from which one item must be chosen Lines of command syntax that wrap should be interpreted as a single command In this document to type text means to type the required text in the specified location and to enter text means to type the required text then press the ENTER key References to literature sources are given in square brackets like this 10 Jaguar 7 0 User Manual xiii xiv Jaguar 7 0 User Manual Chapter 1 Introduction 1 1 About This Manual The Jaguar User Manual is intended to help you perform ab initio calculations for a variety of methods parameters and calculated properties Jaguar can be run from the command line or from the Maestro graphical user interface GUI Online help is available in the GUI although the information in this manual is generally more comprehensive Chapter 2 contains information you will need to run Jaguar including information about using the GUI geometry input formats specifying file names for input and output displaying molec ular geometries symmetrizing geometries and setting run time parameters such as the machine that will perform the calculation We suggest you start by trying the sample calcula tion in Section 2 1 If the calculation runs successfully y
206. asing functions and cutoff parameters used the electrostatic geometry and solvation properties calculated and the parameters used and the output generated gvb Sets GVB pairs Imp2 Sets LMP2 pairs for local local MP2 calculations and delocalization of LMP2 pairs atomic Sets atom specific properties including atomic masses for isotopes van der Waals radii for PBF solvation calculations and basis functions for individual atoms hess Allows input of initial nuclear Hessian guess Allows input of initial wave function pointch Adds independent point charges efields Adds electric field or fields ham Allows user input of Hamiltonian orbman Allows orbitals to be reordered or linearly combined echo One word section indicating that the input file should be echoed in the output file path Specifies execution path listing order of Jaguar programs to be run nbo Requests NBO Natural Bond Orbital calculation core Specifies SCORE keylist for NBO calculation choose Specifies CHOOSE keylist for NBO calculation nrtstr Specifies SNRTSTR keylist for NBO calculation For example amp gen iguess 0 molchg 1 amp sets the iguess and molchg keywords of the gen section to 0 and 1 respectively Sections may span multiple lines and more than one section may appear in a line However a gen section Jaguar 7 0 User Manual 157 Chapter 8 The Jaguar Input File 158 keyword and its value must be on the same line The follow
207. at the row atom and the column atom for the matrix element are the same atom An entry of 1 indicates that the row atom and the column atom are considered to be bonded because they are separated by a distance less than the sum of their covalent radii times the variable covfac which is 1 2 by default and is also described in Section 8 5 2 on page 164 If a connectivity table entry is 2 the corresponding row and column atoms are each bonded to some same third atom by the defini tion of bonding described above An entry of 3 4 or more means that the atoms are within the third fourth or higher neighbor range of each other Geometry optimization details If this option is selected additional information about the progress of a geometry optimization is printed This output often helps reveal the cause of any problems with optimizations Overlap matrix The overlap matrix S for the basis functions is printed in five column blocks if this option is selected Since the matrix is symmetric the upper triangle is not printed One electron Hamiltonian The one electron matrices representing kinetic energy and the sum of kinetic energy nuclear attraction and point charge electron interactions is printed in atomic orbital space in five column blocks if this option is selected Since the matrices are symmetric the upper triangles are not printed Gaussian function list basis set By selecting this option you can print out information about
208. ated into the Project Table Each scan point is added as a separate entry to the table with the energy and scan coordinates as properties If you want to submit a particular scan point to Jaguar for refinement you can select the corresponding entry as the source of job input You can use the plot facility to display plots of the energy as a function of a particular coordinate for example Jaguar 7 0 User Manual 83 Chapter 4 Optimizations and Scans 84 An additional output file with the name jobname steps in is written to the working directory whenever a scan is performed This file contains the geometry specifications for each geometry in the scan along with the calculated energies keywords and forces However it cannot be read into Maestro as it is You can use the UNIX command csplit to break up the jobname steps in file into individual input files any of which can then be modified and submitted to Jaguar Each input section in the jobname steps in file terminates with the string END_OF_INPUT You can use this string to tell csplit where to split the file For example for a jobname steps in file that has 3 input sections in it the command csplit prefixzjobname jobname steps in END OF INPUT creates four files called jobname00 jobname01 jobname02 and jobname03 the last of which contains the last END OF INPUT string and can be deleted After renaming these files so that they have a in extension th
209. ation the fast pseudospectral method or the slower analytic method in which four center two electron integrals are computed explic itly The analytic method is used only when optimized pseudospectral grids and dealiasing function sets for one or more atoms in the molecule are not available For molecules whose atoms are all in the range H Ar in the periodic table we recommend using the 6 31G basis set the default choice which is one basis set that permits pseudospectral calculations The column headed of d fns indicates whether d shells include the five real spherical func tions dy dy dyz dx2 y2 and dz 2_ 2_ 2 all with the same angular momentum 2 or xy yz whether d shells include the six Cartesian d functions d 2 d 2 d 2 dyy dyz and du This xy Jaguar 7 0 User Manual 31 Chapter 3 Options 32 choice also affects the dimension of the Fock matrix for diagonalization To override this selec tion select the Number of D functions option that corresponds to your preference or set the keyword numd in the gen section of the input file as described in Section 8 5 16 on page 192 The orbital coefficients are always printed out in terms of the six Cartesian functions For basis sets with f functions the real spherical set of 7 f functions is always used The references describing the basis sets are in the References list at the back of this manual Table 3 1 Available basis sets that do no
210. ation CI coeff gt 6 0 95735 gt 11 0 26823 Transition dipole moment debye X 0 0000 Y 1 3726 Z 0 0000 Tot 1 3726 Oscillator strength f 0 0671 Excited State 2 11 5077 eV 107 74 nm orbitals in excitation CI coeff 5 gt 7 0 82270 5 gt 10 0 55056 5 gt 14 0 11504 Transition dipole moment debye X 0 0000 Y 0 0000 Z 0 0000 Tot 0 0000 Oscillator strength f 0 0000 From this example the lowest excited state of water is mostly a transition from orbital 5 the HOMO to orbital 6 the LUMO The transition dipole moment is the amplitude that is used to evaluate the oscillator strength which is a measure of the transition probability Oscillator strengths near 1 indicate strongly allowed transitions From the above output an electronic transition to the second excited state of water is not a dipole allowed transition due to symmetry while the transition to the first excited state is predicted to be only weakly allowed 5 3 10 Basis Set If you selected Gaussian function list basis set in the Output tab or set ip1 2 in the gen section a list of atoms and the basis set used for each atom is given followed by two tables that provide information about the basis set The functions in a basis set are made up of polynomials of the appropriate degree multiplied by linear combinations of Gaussian primitives of the form Nexp zr where N is a normaliza tion constant and z is the exponent of the p
211. ations under Linux If you plan to use queueing software the list of host names to be used for each job is determined dynamically by the queue and that list needs to be made available to Jaguar in the SCHRODINGER_NODEFILE environment variable For PBS and SGE queues this is handled automatically in the SCHRODINGER queues queuetype template sh file For LSF and other queues you must determine how the queue stores the list of host names to be used for a job typically by an environment variable and then set SCHRODINGER_NODEFILE to the file that contains that list Each host name in the list must be on a separate line Space separated lists do not work For more information on setting up Schr dinger software to run on a queuing system see Section 3 2 of the Job Control Guide Edit the schrodinger hosts file in the directory where Jaguar was installed and list in it the names of the hosts or queues if appropriate in the machines LINUX file The host names in schrodinger hosts need not include the domain name See the Job Control Guide for details on the format of the schrodinger hosts file For the above example the schrodinger hosts file would look like host homer schrodinger apps Schrodinger tmpdir scr processors 2 host marge schrodinger apps Schrodinger tmpdir scr processors 2 host bart schrodinger apps Schrodinger tmpdir scr processors 1 4 MPICH s p4 communi
212. atoms at the LMP2 level while the remaining atoms are treated at the HF level Local local MP2 calculations use orbitals that are localized on the specified atom pairs After the localization of the canonical Hartree Fock orbitals the atomic orbital coefficients for each localized orbital are summed for each atom and the orbital is considered localized on the two atoms whose coefficient sums are largest If the largest coefficient sum on one atom is more than ten times as large as the coefficient sum on any other atom the localized orbital is considered to be localized on that single atom and that localized orbital will be included in any LMP2 calculation for which that atom is specified in any requested LMP2 atom pairs Jaguar includes a setting for a local LMP2 calculation that treats all atoms bonded to atoms of other elements heteroatom pairs at the LMP2 level These heteroatom pairs do not include C atoms bonded only to C and H atoms so hydrocarbon fragments are not correlated We recommend this setting for solvation calculations using LMP2 To request such a calcula tion select Hetero atom pairs in the LMP2 pairs section For other kinds of local LMP2 calcu lations you must set up the pairs in an Imp2 section by editing the input file See Section 3 5 on page 40 for more information If you add an Imp2 section the Level of theory is set to Other Correlation of orbitals on atom pairs in a virtual space that is restricted to those
213. aximum gradient component rms displacement maximum displacement energy change Jaguar 7 0 User Manual 89 Chapter 5 Output 90 Table 5 1 Options for the jaguar results command Continued Option Meaning Timing options time total cpu time for job tscf total time in sc f cumulative trwr total time in rwr cumulative tderlb total time in der1b cumulative SCF information options iter number of scf iterations Per atom information options atoms atom names atomnums atomic numbers coords cartesian atomic coordinates forces cartesian atomic forces charges ESP atom centered charges Options for printing of title and intermediate results title print column titles titleonly print only the column titles all report results every geometry iteration allscf report results for each scf calculation allderib report results for each der1b 5 1 4 Reporting Final Results From One or More Jobs By default each row of the Jaguar results table except the title row corresponds to the final results from a Jaguar output file that was listed in the jaguar results command For instance if you entered the command jaguar results energy RuCp2 out piperidine out from a directory containing the output files RuCp2 out and piperidine out you would get a very simple table like this 480 726524 250 470399 Jaguar 7 0 User Manual Chapter 5 Output where the first line lists the final
214. ay follow on the same line If any sets are listed after the word BACKUP it indicates that if an atom is not found in the current basis set its basis function will be obtained from the list of backup basis sets If there is more than one backup name listed the basis function for the atom comes from the first backup set listed that contains that atom Note that the numbers of d shells specified in the backup basis sets is ignored Also polarization or diffuse functions are chosen according to the basis set specified by the calculation that is or options on backup basis sets are ignored if they do not agree with the options on the basis set chosen for the calculation The basis set description continues with a set of lines describing the basis functions on each atom The information for each atom begins with a line containing the element symbol e g He The atomic symbol must not be preceded by any spaces or characters The next line begins with the type of function S P or D for instance If this label is SP the corresponding set of data describes an s and a p function whose Gaussians have the same exponents The next number in that line is the polarization diffuse function parameter If it is 1 it indicates a polar ization function which is included in the basis set if the basis set name ends in an as described in Section 3 2 on page 30 If the number is 2 it indicates a basis set function if 1 a basis set function
215. batch script In this case there is no template to be modified You can create the batch script and the Maestro input file from the Jaguar panels in Maestro and submit the batch job for execution or save the files to disk and run them later from the command line or from Maestro If you run remote batch jobs by default the input and output directories must be on a disk system that is available to both the submission and the execution host such as a cross mounted disk or an NFS file system This behavior corresponds to the use of the LOCAL option If you want to remove this restriction run the batch job with the nolocal option The individual jobs in the batch script are run in their own local directories which may be on the remote host 10 2 3 Batch Input File Examples Batch scripts can be used in multiple ways In this section two examples are provided for the following scenarios 1 Pipelined scripts in which the output from one job provides the input to a subsequent job The pKa batch script is an example Here we provide an example that performs an opti Jaguar 7 0 User Manual 277 Chapter 10 Running Jobs 278 mization at a medium level of theory followed by single point calculations at a higher level of theory 2 A script that uses the input files in one directory as templates and writes all new files into the launch directory This kind of script is useful for running jobs with different options on the same struct
216. bitals total 25 number of core orbitals 5 number of open shell orbs 0 number of occupied orbitals number of virtual orbitals 20 number of hamiltonians 1 number of shells 1 SCF type HF i u a i g t p i G r RMS maximum e d i u i energy density DIIS rts td total energy change change error etot 1 N N 5M 75 61350567257 1 6E 02 3 3E 01 etot 2 Y Y 6 M 75 99456008691 3 8E 01 6 2E 03 6 9E 02 Jaguar 7 0 User Manual Chapter 5 Output etot 3 Y Y 6 M 76 01904109359 2 4E 02 1 7E 03 2 9E 02 etot 4 N Y 2 U 76 02333233097 4 3E 03 7 6E 04 4 7E 03 etot 5 Y Y 6 M 76 02361760760 2 9E 04 1 7E 04 1 5E 03 etot 6 Y N 6 M 76 02364072535 2 3E 05 0 0E 00 0 0E 00 Energy components in hartrees A Nuclear repulsion 9 33000672144 E Total one electron terms 123 34165776264 I Total two electron terms 37 98801031585 L Electronic energy 85 35364744679 E I N Total enerqy rie cer e gg 76 02364072535 A L SCFE SCF energy HF 76 02364072535 hartrees iterations 6 HOMO energy 0 49745 LUMO energy 0 21516 Orbital energies symmetry label 20 55693 A1 1 34635 A1 0 71380 B2 0 56828 A1 0 49745 B1 0 21516 A1 0 30862 B2 1 01720 B2 1 09266 A1 1 13459 A1 1 16904 B1 1 29575 B2 1 41126 Al 1 80256 A2 1 82999 A1 end of program scf The output from the program scf begins with a list of information detailing various numbers of electrons orbitals Ha
217. bitals for multiple bonds may therefore be diagonal ized using the one electron Hamiltonians The output for this procedure begins with a table of the Mulliken populations for each orbital on each atom which reveals multiple bonds as described in the following table Every bond pair space made up of all orbitals with signifi cant Mulliken populations on the same pair of atoms is diagonalized and the output indicates the number of these bond pair spaces found and the ordering of the new orbitals by their one electron Hamiltonian values If you choose to print out Boys orbitals by setting the print keyword ip107 to 2 it is these final orbitals which are printed 8 5 20 File Format Conversion Keywords You can call the program Babel 26 from Jaguar to generate files in any of a variety of formats although the files produced by Babel contain only geometries not calculation settings The output can be generated at the end of each iteration in a geometry optimization or at the end of any job To generate such an output file you must set the format keyword for the chosen file type The format keywords and file types supported are shown in Table 8 31 If you want to generate an output file in a particular format only at the end of a job you should use a keyword setting of the form babel outext where outext is one of the possible format keywords listed in Table 8 31 You can set babel more than once using separate babel outext assignments if
218. by setting their nuclear charge to zero in the charge column see Section 8 8 3 on page 222 Jaguar 7 0 User Manual 15 Chapter 2 Running Jaguar From Maestro 16 To automate the calculation of a counterpoise corrected binding energy for a complex consisting of two non covalently bound molecules use the Jaguar batch script called counterpoise py See Section 10 2 4 on page 279 for details For LMP2 calculations see Section 3 5 on page 40 the LMP2 correction is already designed to avoid basis set superposition error so we advise computing only the SCF counterpoise correction term 2 4 8 Specifying Coordinates for Hessian Refinement If you are optimizing a molecular structure to obtain a transition state you might want to refine the Hessian used for the job Section 4 3 on page 74 explains the methods used for transition state optimizations including Hessian refinement This subsection explains only how to edit your input to specify particular coordinates for Hessian refinement Whether or not you refine particular coordinates you can specify a certain number of the lowest eigenvectors of the Hessian for refinement as described in Section 4 3 4 on page 78 the Hessian can be refined in both ways in the same job If you type an asterisk after a coordinate value Jaguar computes the gradient of the energy both at the original geometry and at a geometry for which the asterisk marked coordinate has been changed slightl
219. c corrections of the form lt aalaa gt calculated for K 2 Diatomic analytic corrections of the form aalaa aalab lt aalbb gt and lt ablab gt calculated for K a a b and c refer to distinct atoms 9 6 The Lewis File The Lewis file determines how van der Waals radii for calculations using the Jaguar solvation module are set according to chemical functional groups By default for neutral molecules in water the program calculates a Lewis dot structure for the molecule or system scans the Lewis file for radius information for each atom and sets radii for relevant atoms then sets any radii not determined by the Lewis file according to the atomic section or the standard default value Settings for radii not included in the Lewis file are described in Section 3 9 on page 48 and Section 8 8 on page 219 and are listed in Table 8 44 on page 224 If you do not want the atomic radii that determine the dielectric continuum boundary to change according to the chemical environment of the atom set the solvation keyword isurf to 0 in the gen section Otherwise Jaguar will alter some radii for neutral molecules by using the default lewis file from the data directory unless you specify your own lewis file in a LEWISFILE line in the input file as described in Section 8 1 on page 155 If radii are set according to a Lewis file Jaguar first computes a Lewis dot structure for the input geometry to determine each atom s bonds and hybridizati
220. c pVTZ f H Ar Ca H C Ne Si Ar Br pseudospec 5 101 without f Ga Kr tral others analytic 104 functions cc pVQZ g H E Na Ar H C O pseudospectral others 5 101 without g Ca Ga Kr analytic analytic functions MIDIX H Li C F H C F P Cl pseudospectral Li 5 105 Si Cl Br I Si Br I analytic 107 TZV H Kr rh Sc Zn analytic 5 108 p only TZV f H Kr Sc Zn p analytic 5 108 and f a This basis is referred to in the literature as 6 311G 3df 3pd The other available basis sets which are listed in Table 3 2 include effective core potentials ECPs The names of eight of these basis sets begin with LA to indicate they were devel oped at Los Alamos National Laboratory If the next character in the name is a V the basis set is valence only containing only the highest s and p shells for main group atoms and the highest s p and d shells for transition metals For example 5s and 5p would be included for tellurium and 6s 5d and 6p for tungsten LAV1 indicates that the basis set has been fully contracted to form a minimal basis set LAV2 that the last Gaussian has been uncontracted to form a double zeta basis and LAV3 that all of the s functions and the last p and d Gaussian have been uncontracted Names starting with LACV indicate that the basis set also includes the outermost core orbitals e g 5s5p6s5d6p for W The last letter in each LA basis set name refers to the bas
221. cal LMP2 calculations full local LMP2 energy correction is sum of pair ener gies ip173 Fock matrix in Boys localized orbital space ip192 2 Extra optimization related information such as the quadratic energy error 3 Same as setting ip192 2 but includes more detailed information such as the Hessian ip193 2 Numerical Hessian in freq output Jaguar 7 0 User Manual 205 Chapter 8 The Jaguar Input File 206 Table 8 32 Output keywords and their settings Continued Keyword Value Description ip194 2 Diagonal force constants in internal coordinates 3 Same as setting ip194 2 but also includes off diagonal force con stants if they are larger than a factor 0 01 by default times the geo metric mean of the corresponding off diagonal elements the value of the factor can be set using the opt194 keyword 4 All diagonal and off diagonal force constants are printed a When any of the keywords is set equal to 1 the corresponding output is not generated 8 5 22 File Output Keywords The file output keywords are the options that cause files other than the usual log and output files to be created All but one of these keywords are set to 1 by default meaning that the file is not created The file output keyword ip151 controls whether or not a Jaguar restart file is written It is the only file output keyword whose default value of 1 indicates that it is on When ip151 is set to 1 the file restart inis created in the temp direc
222. cal space and transformed back into spectral space by the following equations Se m Yel Y Au Du R 3a g kl Kj BON Dina Panne 3b g n m where D is the usual spectral space density matrix R is the value of the function j at grid point g and A klg is given by Equation 2 The grid points used for each SCF iteration are Jaguar 7 0 User Manual Chapter 7 Theory determined by the grid type coarse medium fine or ultrafine chosen for that iteration The number of arithmetic operations involved in the assembly of the matrices J and K in Equation 3a and Equation 3b scales formally as N as opposed to the N scaling for the matrix assembly in the conventional spectral space algorithm Jaguar actually uses the pseudospectral method described above for the majority of the compu tationally intensive two electron integral terms but calculates the one electron and some of the largest and most efficiently computed two electron terms analytically 13 For the Coulomb matrix elements we calculate the analytic terms Y GAD y kl for cases in which i j k and meet certain cutoff criteria and the two electron integral ijlkl is of the form aalaa aalab aalbb ablab or aalbc where a b and c indicate the atom upon which the function is centered Similar correction terms are computed for the exchange operator as detailed in ref 13 The corresponding pseudospectral terms as defined by Equation 3a and Equation
223. cates the end of the hybridization type information as for the bonding type information The beginning of the hybridization information in a sample lewis file illustrating a list of hybridization type information for hydrogen and carbon is shown below with some comments to further explain the file format HYBRIDIZATION TYPE 01 INFORMATION 1 HYDROGEN Group 1 H C sp2 bonds 1 hybridization sp2 hybridization sp2 hybr MUST have 5 spaces before it 1 element 6 Group 2 H O sp3 bonds 1 hybridization sp3 hybridization 1 element 8 KKK 6 CARBON Group 1 C C sp3 bonds 1 hybridization sp3 hybridization 1 atom 6 The number of spaces at the beginning of the lines described above is irrelevant for all lines except the Group lines and the hybridization labels After all desired hybridization types are described for all appropriate elements the hybridiza tion type information should end with a blank line 9 6 3 Setting van der Waals Radii From Lewis File Data The Lewis file can be used to make non default choices for van der Waals radii of atoms in particular chemical environments or even to reset the default radii for particular elements After the lewis program analyzes an input geometry s Lewis dot structure it sets the atom s van der Waals radius to the value dictated by the first atom type description of element and chemical environment in the Lewis file that matches that atom with no contradiction If no
224. cating Newton Raphson step s 1 Apply trust radius by level shifting of Hessian to reduce resultant step size Jaguar 7 0 User Manual 181 Chapter 8 The Jaguar Input File 182 Table 8 20 Keywords for trust radius adjustment Continued Keyword Value Description trust 0 3 Initial trust radius in atomic units bohr and or radians if norm of pro posed displacements exceeds trust radius step size is reduced as described by itrcut default is 0 3 except for solvated cases or transition state optimizations when it is 0 1 tradmx 0 3 Maximum trust radius allowed during optimization for itradj gt 0 see trust information default is 0 3 except for solvated cases when it is 0 1 tradmn 0 01 Minimum trust radius allowed during optimization for itradj gt 0 see trust information tremx 0 25 Trust radius reduction criterion if relative error between actual and pre dicted energy changes is more than tremx and itradj gt 0 trust radius is reduced trgmx 0 0 Trust radius reduction criterion for itradj gt 0 and trgmx gt 0 if absolute error in a component of predicted gradient exceeds trgmx hartrees bohr trust radius is reduced treok 0 2 Criterion for increasing trust radius if itradj 2 and relative error between actual and predicted energy changes is less than treok trust radius is increased treok default is 0 2 trescal 2 0 Scale factor for trust radius adjustment used only when itradj 2 The keywords sh
225. cation device relies on either rsh or ssh so one of these must be enabled to work without passwords rsh is the default but if you built MPICH using Jaguar 7 0 User Manual 295 Chapter 12 Parallel Jaguar 296 RSHCOMMAND ssh then ssh will be used Even if you built MPICH to use rsh you can still use ssh if you set the environment variable P4_RSHCOMMAND ssh before launching Jaguar MPICH s secure server daemon serv_p4 is used to transmit the environment from the master node to the slave nodes and this daemon uses ruserok for client authentication This means that either the etc hosts equiv file must list all hosts in the cluster or the user must have an rhosts file in his or her home directory The rhosts file must contain the name of each host on which parallel calculations will be run followed by the user s login name e g homer mynet edu username marge mynet edu username bart mynet edu username The rhosts file must be owned by the user not by root and must not be writable by anyone except the user or authentication fails To ensure this enter the command chmod 644 rhosts See the man page on ruserok for more information We strongly recommend that you test rsh or ssh connections by using the shell script tstmachines which is in MPICH_install sbin This script attempts to run several rsh or ssh commands on each of the hosts listed in the file machines LINUX and lists any prob lems If the comman
226. ccurate enough for the desired symmetry to be recognized You can symmetrize the molecule using the Symmetrize Workspace toolbar button in the Build panel A When you click this button the Symmetrize Workspace dialog box is displayed The point group symmetry is determined as follows After the molecule is translated so that the center of mass is at the origin of the coordinate system and rotated so that the principal axes of inertia are aligned on the coordinate axes symmetry operations reflections rotations and inversions are applied to determine the point group of the molecule 4 Keyword isymm 8 in the gen section Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro 20 _ Symmetrize Workspace Tolerance 0 04 Point Group tolerance 0 04 Cs Symmetrize Close Help i Figure 2 4 The Symmetrize Workspace dialog box When Maestro checks whether a symmetry operation produces an equivalent structure the coordinates of the two structures only have to be the same to within a prescribed tolerance that is each pair of symmetry related atoms is within a distance specified by the tolerance The value of the tolerance can be specified in the Tolerance text box and is 0 04 A by default This value ensures that the highest symmetry is found in most cases By changing the value and clicking the Find Point Group button you can determine whether there is a lower or higher symmetry po
227. clear attraction integrals and point charge terms separate Note if isolv 1 or 2 kesep 1 by default isolvg 0 Compute gradients in solvent with method used in Jaguar 3 5 and ear lier 1 Compute gradients in solvent with more robust method for Jaguar 4 0 on epsout 80 37 Outer dielectric constant of solvent epsin 1 0 Inner dielectric constant of solvent 173 radprb 1 40 Radius of solvent probe molecule sconv 1 5x10 Solvation energy convergence criterion in Hartrees esolv number Gas phase energy of molecule in Hartrees used in some restart new input files for solvation jobs solvent string Solvent name water benzene chlorobenzene cyclohexane carbon tet carbon tetrachloride dichloroethane 1 2 dichloro ethane methanol nitrobenzene dmso dimethyl sulfoxide chloroform dichloromethane dimethyl formamide tetrahydrofuran 8 5 14 Properties Keywords Keywords to request calculation of molecular properties including multipole moments and charge fitting properties are listed in Table 8 25 most of which correspond to GUI options described in Section 3 10 on page 52 Only the values listed in the table are allowed Analytic polarizabilities o and hyperpolarizabilities B and y are available for HF UHF DFT and UDFT methods The definition of B changed with Jaguar 5 5 and differs by a factor of 0 5 from that used in previous versions of Jaguar The new definition is now consistent with that used in GAUSSIAN The definition
228. coarse grid for electron density calculations and the ultrafine grid for gradient calculations and the extreme grid is included for testing purposes so the number of grid types in the file default grid is actually five Jaguar uses the grids upon each atom in the molecule provided by the grid file to generate molecular grids All grids for each basis set are then listed in turn The basis set is identified with a BASIS line and containing its name and is followed by a blank line Each molecular grid description starts with two comment lines usually a blank line followed by a descriptive line The next line contains an integer flag which determines which points from the atomic grids for the atoms in a molecule are included in the molecular grid Jaguar generates a boundary plane between the two atoms and perpendicular to the vector between them disposing of any points from one atom that are on the other atom s side of the boundary plane The integer flag determines the location of this plane if the flag is 0 the plane is located so that the ratio of the distances of the atoms to the plane is the same as the ratio of their cova lent radii while if it is 1 the boundary plane is set where the grid point density from each atom on the vector between the atoms is equal The grid point density is determined as a spline fit of the density for each shell where each shell s density is determined as the number of points for that shell divided by the sh
229. complete Z matrix for the example molecule the 150 conformation of glycine is N1 C2 N1 1 4589 C3 C2 1 5203 N1 115 32 04 C3 1 2036 C2 126 28 N1 150 0 O05 CH 1 3669 C2 111 39 Nl 31 8 H6 Nl 1 0008 C2 113 55 C3 69 7 H7 N1 1 0004 C2 112 77 C3 57 9 H8 C2 1 0833 N1 108 89 H6 170 0 H9 C2 1 0782 N1 110 41 H6 52 3 H10 05 0 9656 C3 111 63 C2 178 2 2 4 5 Variables and Dummy Atoms in Z Matrix Input Bond lengths or angles can also be specified as variables below the Z matrix itself This feature makes it easier to input equal values such as C H bond lengths or H C H bond angles for methane and also makes it possible to keep several distances or angles the same as each other during an optimization To use variables type the variable name chbond for instance where you would type the corresponding value such as a C H bond length in for each relevant occurrence of that value You can prefix any variable with a or sign After you type the full Z matrix define the variables by adding one or more lines at the bottom such as chbond 1 09 HCHang 109 47 As for Cartesian input you can separate the variable settings from the coordinates by a line containing the text Z variables Defining dummy atoms can make the assignment of bond lengths and angles easier Dummy atoms are a way of describing a point in space in the format used for an atomic coordinate without placing an atom at that point The symbols allowed for dummy at
230. ctional occupation number pFON method for thermal smearing 148 fdtemp 10000 Initial temperature in K for thermal smearing 196 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 28 Keywords for methods used in the SCF convergence procedures Continued Keyword Value Description icanorb 0 Allow number of canonical orbitals to vary during calculation 1 Fix number of canonical orbitals during calculation ncanorb 20 Number of canonical orbitals to keep during calculation Another method for controlling SCF convergence is thermal smearing 148 which improves convergence in difficult cases by using a fictitious temperature to fractionally occupy all orbitals occupied and virtual and then decrease the temperature until convergence is reached The orbital occupation numbers are represented by a Fermi Dirac function n 1 1 exp e kT Two methods for determining the occupation numbers have been implemented FON fractional occupation number and pFON pseudo FON In the FON method the Fermi energy is determined so that the resulting occupations sum to the total number of electrons In the pFON method a Fermi energy is assigned halfway between the HOMO and LUMO energies and then the resulting occupations found from this Fermi energy are renormalized so that they sum to the total number of electrons Thermal smearing is turned on using the keyword ifdtherm A value of 1 selects the FON method a valu
231. culation along with information about the electric fields used for the dipole calculations An example of output from a polarizability and hyperpolarizability calculation follows polarizability in AU alpha x x 5 551 alpha x y alpha y x 0 000 alpha y y alpha z x 0 000 alpha z y 0 000 alpha x z 0 000 5 245 alpha y z 0 000 0 000 alpha z z 11 890 alpha 7 562 Dalpha 6 497 first hyperpolarizability in AU beta x x x 0 000 beta y y y 0 000 beta z z z 10 206 beta x y y 0 000 beta x z z 0 000 beta y x x 0 000 beta y z 0 000 beta z x x 0 435 Jaguar 7 0 User Manual 111 Chapter 5 Output 112 beta z y y 0 404 beta x y z 0 000 sum beta x 0 000 sum beta y 0 000 sum beta z 9 367 beta 5 620 second hyperpolarizability in AU gamma x x x x 9 110 gamma y y y y 11 758 gamma z z z z 28 020 gamma x x x y 0 000 gamma x x x z 0 000 gamma x x y y 1780 861 gamma x x y z 0 000 gamma x x z z 2 950 gamma x y y y 0 000 gamma x y y z 0 000 gamma x y z z 0 000 gamma x z z z 0 000 gamma y y y z 0 000 gamma y y z z 5 235 gamma y z z z 0 000 gamma 718 848 After the tensor matrix elements the program prints various sums of these matrix elements For the polarizability the quantities o and Aa are reported as alpha and Dalpha defined as follows O t Apy 0 3 2 2 2 AQ Jo 0 Dal 0 Oyy
232. cutables By default Jaguar looks for the executables available for the machine upon which you want to run a Jaguar job then uses the most recent Jaguar executables for that machine type However if you have several differing sets of Jaguar executables at your site such as different versions of Jaguar or executables for different machine types you can choose to run your Jaguar job with a non default choice of executables To determine which sets of Jaguar executables are available enter the command jaguar LIST to find out about executables on the current host or jaguar LIST HOST hostname to find out about executables on another machine 10 1 3 Running a Jaguar Job From the Command Line The jaguar run command lets you run a Jaguar job using the Jaguar input file you specify and any of the jaguar run command options shown in Table 10 2 and described below The first three options are common to all Schr dinger programs You can also use the Job Control version options Note The single letter options h and v are no longer supported The options F n p s and w are still supported but we cannot guarantee that they will continue to be supported You should use the new equivalents To run a Jaguar job you first need a Jaguar input file The file should be named in the form jobname in You can create an input file using the GUI see Section 2 3 on page 8 for more information If you create or edit an input file using a
233. d ROHF treatment of open shell molecules the controls available when you choose HF Hartree Fock from the Level of theory option menu allow you to set up configuration interaction singles CIS calculations for excited states These calculations are only available for a closed shell Hartree Fock reference wave function To do a CIS calculation select Excited state CIS You can then enter the number of states you want to generate in the Number of excited states text box and set a limit on the number of iterations in the diagonalization procedure in the Maximum CIS iterations text box 7 You should consider including more excited states than you need to ensure that you include the states of interest and cover any near degeneracies 3 5 Local MP2 Settings The LMP2 Local MP2 option of the Level of theory option menu allows you to set up a local Mealler Plesset second order perturbation theory 57 60 calculation The local MP2 LMP2 method greatly reduces the basis set superposition errors that can arise from the canonical MP2 method 60 The LMP2 method is much faster than canonical MP2 and typically recovers 9846 of the canonical MP2 energy correction The pseudospectral implementation of LMP2 is described in Section 7 4 on page 149 For closed shell systems you can perform LMP2 geometry optimizations charge fitting solvation calculations and many other options available with HF wave functions For open shell systems you can perfor
234. d DeltaG S are listed in the final three rows Delta EN is the energy difference between the total internal energy in the solution phase E EN liq and the total energy in the gas phase E EN g This energy should always be positive because it represents the energy that was spent distorting the optimized gas phase molecular orbitals in order to polarize the molecular system Del taG ENP is the solvation free energy computed without adding first solvation shell contributions The final value listed this table De1taG S is the standard state free energy of solvation of the system for a temperature of 298 K and for a standard state that uses a concentration of 1 M in both the gaseous and solu tion phases Jaguar 7 0 User Manual Chapter 5 Output After the various components of the solvation free energy have been printed out molecular properties in the solution phase are printed out from the program ch These have the same form as for the gas phase properties shown above For expert users advanced output can be obtained by specifying ip378 2 in the gen section of the input file When this option is specified the gas phase and solution phase Mayer bond order matrix the atomic radii used to calculate G P liq and G CDS liq a breakdown of G CDS liq and G P liq by atom and a table listing the individual contributions to G CDS 1iq are printed out 5 3 6 Geometry Optimization in Solution Geome
235. d be used Alternatively you may leave the values blank for values at the Jaguar 7 0 User Manual 219 Chapter 8 The Jaguar Input File 220 end of the row For instance either of the sections below has the same effect as the first atomic section example listed above amp atomic atom mass vdw2 H1 2 00 1 20 H2 2 00 1 20 0 1 55 amp amp atomic atom vdw2 mass H1 1 20 2 00 H2 1 29 2 00 O 155 amp Atoms may be described in more than one set of atomic input values but the same keyword cannot be used more than once for the same atom For example the following syntax is supported amp atomic atom basis C1 6 31g atom formal CL 3 amp but the following syntax is not supported amp atomic atom basis C1 6 31g atom basis C1 cc pVTZ amp To print an atomic section in the restart file that contains information for all atoms not just some set the output keyword ip29 to 2 If an atomic section exists or if ip29 2 in the input file the atomic section is echoed in the output from the program pre 8 8 2 Keywords That Specify Physical Properties The keywords that specify physical properties of atoms are listed and defined in Table 8 42 Values for these keywords can appear in restart files The formal keyword is useful for solvation jobs because the van der Waals radii are adjusted according to the chemical structure found by Jaguar and for generating an improved initial Jaguar 7 0 User Manu
236. d is a combination of b for exchange and p86 for correlation Table 8 8 Standard functional names for the dftname keyword Name Description hfs Slater local exchange functional 34 xalpha Xa local exchange functional 34 hfb Slater local exchange functional 34 Becke 1988 non local gradient correction to exchange 37 hfpw Slater local exchange functional 34 Perdew Wang 1991 GGA II nonlocal exchange 36 bp86 vwn5 Exchange Slater local functional 34 Becke 1988 non local gradient correction 37 correlation Vosko Wilk Nusair VWN local functional 35 Perdew 1986 gradient correction functional 40 pwpw91 Exchange Slater local functional 34 Perdew Wang 1991 gradient correction functional 36 correlation Perdew Wang 1991 GGA II local and nonlocal func tionals 36 hcth407 Hamprecht Cohen Tozer Handy functional including local and nonlocal exchange and correlation reparametrized with a training set of 407 molecules by Boese and Handy 46 pbe Perdew Burke Ernzerhof local and nonlocal exchange and correlation functional 47 b3lyp Exchange exact HF Slater local functional 34 Becke 1988 nonlocal gradient correction 37 correlation Vosko Wilk Nusair VWN local functional 35 Lee Yang Parr local and nonlocal functional 38 Jaguar 7 0 User Manual 169 Chapter 8 The Jaguar Input File 170 Table 8 8 Standard functional names for the dftname keyword Continued Name Description
237. d is successful it returns with no output You can also use the v option on the command line to see exactly what the script is doing 12 1 2 3 Launching the Secure Servers Jaguar relies on the MPICH secure server serv_p4 to transport the environment to all nodes used in a parallel calculation The secure server must be running on all computers on which Jaguar is to run in parallel which is normally all hosts listed in the machines LINUX file The secure server uses a communication port that is specified by the user or by root To use the secure servers set the following environment variables in your shell startup script either bashrc or cshrc csh tcsh setenv MPI USEPASSPORT yes setenv MPI PASSPORT port setenv SCHRODINGER MPI START yes sh ksh bash export MPI USEPASSPORT yes export MPI_P4SSPORT port export SCHRODINGER MPI START yes The port number port should be a four digit number greater than 1023 In principle the root user could set the two MPI variables in the default environment for all users All users would Jaguar 7 0 User Manual Chapter 12 Parallel Jaguar then use the same communication port In practice however we have received reports that this does not always work presumably because of security blocks of some kind With the setting SCHRODINGER_MPI_START yes the default value Jaguar launches the secure server daemons automatically on all nodes to be used for the job It is also
238. d orare gera e Y Mp Rr EA DERE A 176 8 5 10 Geometry Optimization and Transition State Keywords 177 8 5 11 Geometry Scan Keywords asics issssstesssas ses teintes b sk ose d s edid oed EpL EP a0 da 183 8 5 12 Intrinsic Reaction Coordinate IRC Kevwords 184 8 5 13 Solvatiori KeyWords E 186 8 5 14 Properties KeyWolds sn ice tri p eie pe min A 187 8 5 15 Frequency Related Keywords eeeeeeeeeenee 191 8 5 16 Basis Set e y WOFEIS ics UEM Mrd eM M atq RU EM A pM SES 8 5 17 Keywords for SCF Methods 8 5 18 Initial Guess Keywords 8 5 19 Localization Keywords a cccccisscccsccesessssasssccssetasescesectieds sane th sat h aset tacet bann raa RE 8 5 20 File Format Conversion Keywords eeccececeseceeesereeeneseeeeseeseeeeseeenneeaers 201 8 5 21 Standard Output Keywords inier ttr ette hectares 204 8 5 22 File Output Keywords iret trn eit tb sett tbe Pie eH I bna ioiai 206 8 5 23 Output Keywords for Each Iteration keen 207 8 5 24 Orbital Output e E 207 8 5 25 Grid and Dealiasing Function KeywordS sees 210 8 5 26 Memory Use KeywOLIds icon eto tease tla ted etos Lau Su eege uESgen 212 8 527 Plotting He EE 214 8 6 The gvb RE EE 217 Erde ge E LI EE 218 8 8 The atomic Section o op Gene ars ace a Dese puebla eee 219 8 8 1 General Format of the atomic Section ANEREN 219 8 8 2 Keywords That Specify Physical Propertes A 220 Jaguar 7 0 User Ma nual
239. d possibly turn the symmetry option off as well The calculation is not what you expected it to be If you read in a Jaguar input file some of the settings in the file take precedence over settings previously made in the GUI See Section 2 5 on page 17 for more details Also certain settings affect other settings auto matically for instance if you choose to calculate polarizabilities the energy conver gence criterion can be reset to 1 0 x 10 For a GVB job the program exits early and the output states that you need a different number of lone pairs on a particular atom As described in Section 6 4 on page 136 you must specify lone pairs for either all or none of the lone pairs on any particular atom Change the lone pair information and try running the calculation again Jaguar 7 0 User Manual Chapter 11 Troubleshooting The SCF calculation does not converge properly or frequencies or other properties look wrong If the geometry entered is of poor quality the calculation may not converge prop erly which may also lead to inaccurate calculation of molecular properties If you are performing a geometry optimization check to see whether the geometry changes are rea sonable if you are performing a single point calculation make sure the structure entered is appropriate You might want to minimize the structure with a molecular mechanics program first If the structure is reasonable convergence problems should not occur and w
240. d some of their applications Their titles are included in the listings The other listings in this section are referenced throughout this manual 1 10 11 Friesner R A Solution of Self Consistent Field Electronic Structure Equations by a Pseudospectral Method Chem Phys Lett 1985 116 39 Friesner R A Solution of the Hartree Fock equations by a pseudospectral method Application to diatomic molecules J Chem Phys 1986 85 1462 Friesner R A Solution of the Hartree Fock equations for polyatomic molecules by a pseudospectral method J Chem Phys 1987 86 3522 Friesner R A An Automatic Grid Generation Scheme for Pseudospectral Self Consis tent Field Calculations on Polyatomic Molecules J Phys Chem 1988 92 3091 Ringnalda M N Won Y Friesner R A Pseudospectral Hartree Fock calculations on glycine J Chem Phys 1990 92 1163 Langlois J M Muller R P Coley T R Goddard W A III Ringnalda M N Won Y Friesner R A Pseudospectral generalized valence bond calculations Appli cation to methylene ethylene and silylene J Chem Phys 1990 92 7488 Ringnalda M N Belhadj M Friesner R A Pseudospectral Hartree Fock theory Applications and algorithmic improvements J Chem Phys 1990 93 3397 Won Y Lee J G Ringnalda M N Friesner R A Pseudospectral Hartree Fock gradient calculations J Chem Phys 1991 94 8152 Friesner R A New Methods for
241. dinate scan from the Jaguar submenu of the Applications menu The Jaguar panel opens with the tabs that are relevant to the chosen coordinate scan type After you have made settings in the other tabs you can set up the coordinates and their values in the Scan tab Coordinates can be added to the scan using the Add New Coordinate section and picking atoms or bonds in the Workspace To set up a coordinate first choose a coordinate type from the Type option menu The allowed coordinate types and the number of atoms to pick for each are Cartesian X X coordinate of an atom Pick one atom Cartesian Y Y coordinate of an atom Pick one atom Cartesian Z Z coordinate of an atom Pick one atom Distance Distance between two atoms Pick two atoms or one bond Angle Angle between three atoms Pick three atoms or two bonds Dihedral Dihedral angle between four atoms Pick four atoms or three bonds When you have chosen a coordinate type select Pick and choose an object from the Pick option menu You can pick Atom for Cartesian coordinates and Atom and Bond for all other types of coordinates If you pick atoms for a distance angle or dihedral they need not be bonded to each other The atoms are marked in the Workspace as you pick them and each coordinate is marked in the Workspace and entered in the Defined coordinates table as it is completed Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans Jaguar jaguar a Use structures f
242. dinger software To set this variable enter the following command at a shell prompt csh tesh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory Once you have set the SCHRODINGER environment variable you can start Maestro with the following command SSCHRODINGER maestro amp It is usually a good idea to change to the desired working directory before starting Maestro This directory then becomes Maestro s working directory For more information on starting Maestro including starting Maestro on a Windows platform see Section 2 1 of the Maestro User Manual 1 3 Citing Jaguar in Publications The use of this product should be acknowledged in publications as Jaguar version 7 0 Schrodinger LLC New York NY 2007 Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro The Maestro interface to Jaguar can simplify the preparation and submission of jobs You can run Maestro on one machine display it to another and start a Jaguar calculation on yet another machine The main part of the interface is the Jaguar panel which you use to prepare job input Without the Jaguar panel you would have to create input files with particular formats in order to run Jaguar Maestro creates these input files for you based on information you provide and submits the job This frees you from learning the input format and program sequences and instead allows you to concentrate on the sci
243. e If the acid and base conformations are different you can specify input files for both the acid and the base If you do you must give two filenames in one of the following forms acidfile deprot basefile basefile prot acidfile prot acidfile deprot basefile deprot basefile prot acidfile Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module The input file name for the acid is acidfile in the input file name for the base is basefile in In this description acid means either the acid or the protonated base and base means the base or the deprotonated acid The structures that are specified in these files must have the same protonation state Thus if you specify an acid in acidfile in the file basefile in must also contain a structure for the acid but in the conformation that is appropriate to the conjugate base Jaguar automatically changes the protonation state and adjusts the charge when it uses these structures The same rules apply to the structure as for a single input file if you are doing calculations for an acid both structures must be protonated and if you are doing calculations for a base both structures must be deprotonated So for example if you performed a conformational search with Macro Model on an amine and its corresponding ammonium ion you would have to remove a proton from the ammonium ion structure before putting it in the acidfile in input file The number of processors used
244. e if the basis set contained contracted functions for 1s 2s and 2p orbitals the derivatives would be listed in the following order a p type function resulting from the derivative of the 1s func tion a p type function resulting from the derivative of the 2s function an s type function resulting from the first term of the derivative of the 2p function and a d type function resulting from the second term of the derivative of the 2p function The last six lines of the sample daf file correspond to the gradient dealiasing function set for He note that the atomic number specified for those five dealiasing function sets was 2 The first line of this set describes this set s long range dealiasing functions centered on the He atom which will be used when coefficients for long range basis functions are to be calculated as explained above The second value on this line 3 dictates that uncontracted s type and p type 1 2 3 basis functions are to be constructed using the second exponent provided for this atom 0 145957 The second line of the set which describes this set s He centered dealiasing functions to be used when calculating the coefficients for He centered short range basis functions the home atom line of the set has a value of 1 entered in the eleventh column meaning that an s type contracted function will be calculated using the exponents provided for the first contracted function for He in the basis set Since this basis set only p
245. e are now interfaces to the jobcontrol command with Jaguar selected as the program For instance jaguar jobs actually executes jobcontrol list program jaguar In addition to running the commands listed in Table 10 1 you can use the jaguar command with the standard Job Control options listed in Table 4 3 and Table 4 4 of the Job Control Guide to obtain information about Jaguar versions and hosts available To find out about versions available on remote hosts you can add the qualifier HOST hostname For example to check whether version 4 2 of Jaguar is installed on the host reda you could use the following command jaguar WHICH HOST freda REL v42 Further examples are given in the next few sections 10 1 1 Selecting an Execution Host If Jaguar is installed on several machines at your site you can use the jaguar command to help determine which host you should use to run your job To determine which local machines are available for running Jaguar jobs enter the command jaguar HOSTS The hosts listed are those in the schrodinger hosts file that are being used by the jaguar command If you find that the list of hosts is incomplete you may need to edit the schrodinger hosts file indicated on the first line of the command output See Section 2 1 of the Job Control Guide for a description of the schrodinger hosts file Jaguar 7 0 User Manual 265 Chapter 10 Running Jobs 266 10 1 2 Selecting Particular Jaguar Exe
246. e Jaguar Input File 194 related molecules while iacscf 3 was effective for graphitic systems Energies obtained with iacscf 2 or 3 can be directly compared to energies obtained without using iacscf Energies obtained using iacscf 1 or 4 can only be compared to other energies obtained using the same value of iacscf because these two settings reduce the number of canonical orbitals used Table 8 28 Keywords for methods used in the SCF convergence procedures Keyword Value Description iuhf 0 Restricted open shell ROHF or RODFT calculation 1 Unrestricted UHF or UDFT calculation iconv 0 Convergence via Fock matrix diagonalization 1 DIIS convergence scheme default choice for most non GVB calculations see iconv 4 3 OCBSE convergence scheme 4 GVB DIIS convergence scheme default for GVB open shell singlet cal culations and calculations whose initial guess is obtained from H maxit 0 Calculate energy but do not update wave function do only one iteration EM Perform a maximum of maxit SCF iterations default value is 48 newcon 0 Use physical constants and conversion factors equivalent to those used in GAUSSIAN 86 1 Use physical constants and conversion factors equivalent to those used in GAUSSIAN 88 90 92 iacc 1 Only ultrafine grid used tight cutoffs Set automatically when large energy changes and oscillations are detected 2 Accurate mixed grid types accurate cutoffs default choice for transition
247. e basis set or sets The other table entries provide the same information as that given in the previous table except that the polarization functions are only applied to atoms obtained from the non ECP basis sets with the exception of the ERMLER2 basis sets All ECP basis sets use five d functions as described earlier in this section Currently the LACVP LAV3P LACV3P and CSDZ basis sets use the pseudospectral method while all other ECP basis sets use the analytic method with the exception of Br and I in the cc pVTZ pp and cc pVTZ pp f basis sets We strongly recommend using either the LACVP or the LACV3P basis set for non lanthanide molecules containing atoms beyond Ar in the peri odic table especially for studies involving charge transfer d metals or correlated wave func tions The LACV3P basis set seems to give substantial improvements over the LACVP basis set for HF LDA and B3LYP atomic state splittings The LACV3P basis set which includes a diffuse d function on any metal atoms is useful for calculations on anions or low spin M 0 complexes of the late first row metals 3 3 Density Functional Theory DFT Settings The density functional theory module in Jaguar allows you to employ a variety of functionals to describe exchange and correlation for either open or closed shell systems The theory is described in Section 7 5 on page 152 This section describes how to set up a DFT calculation in Jaguar You can perform DFT geometry
248. e default value is 0 006 au If you want to print out the electrostatic potential at grid points that you specify add the keyword settings gcharge 6 and ip172 2 to the gen section of your input file The gcharge 6 setting instructs Jaguar to use the grid points and weighting factors in a file whose name and location are specified by the GPTSFILE line in the input file see Section 8 1 on page 155 The ip172 2 setting instructs Jaguar to write out a file named jobname resp containing the electrostatic potential data see the text under Table 8 33 Gas phase NMR shielding constants are available for closed shell and unrestricted open shell wave functions To calculate chemical shifts you should calculate NMR shielding constants for the reference molecules for each element of interest in the same basis set and with the same method as for the molecule of interest By default shieldings are calculated for all atoms including those with ECPs Shielding constants for atoms whose core is represented by an ECP should be treated with caution because the main contributions come from the core tail of the valence orbitals which is largely absent at ECP centers Chemical shifts derived from these shielding constants might display the correct trends but are likely to have the wrong magnitude Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File 8 5 15 Frequency Related Keywords For jobs that include a calculation of vibrational frequenci
249. e exchange matrix K is restricted to the dimensions of the virtual space corre sponding to the occupied localized molecular orbitals i and j The simplest updating scheme for the coefficients is to obtain updated coefficients C if iteratively from the equation T Gr CA IJ m 20 jt j E where and e are the matrix elements F and F in the localized molecular orbital basis and and are the eigenvalues of the Fock matrix in the local virtual basis From the C coefficients and the exchange matrices K Jaguar computes the second order 2 energy CORTE OR E from the equations E EKC a 21a i2j 148 4G 2 21b where the bracket in Equation 21a denotes a trace and 8 is 1 if i j and O otherwise Computing the exchange matrix elements for Equation 21a is approximately 80 of the work for an energy correction computation while generating the C coefficients comprises about 2096 of the work Jaguar performs localized MP2 calculations using pseudospectral methods evaluating inte grals over grid points in physical space in a manner similar to that described for HF and GVB calculations in Section 7 1 on page 141 and Section 7 2 on page 143 The two electron exchange integrals needed for Equation 21a are evaluated over grid points g as follows Jaguar 7 0 User Manual 151 Chapter 7 Theory 152 Pa _ Ki m yo m m 22 g where Q is the least squares fitting operator for molecul
250. e initial Hessian using Murtagh Sargent updates 142 nhesref gt 0 Number of lowest frequency Hessian eigenvectors used in Hessian refinement default is 0 pertnd 0 05 Displacement in atomic units used for Hessian refinement or calcula tions of numerical forces or frequencies ihuptyp 0 Don t update Hessian 1 Update Hessian each iteration using BFGS Broyden Fletcher Goldfarb Shanno method 143 default for minimum energy structure optimiza tions 2 Update Hessian using Powell method 140 3 Update Hessian using mixed Murtagh Sargent Powell method 141 default for transition state optimizations 4 Update Hessian using Murtagh Sargent method 142 not recom mended 1 Compute quantum mechanical Hessian at each geometry sets inhess 4 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 19 Keywords for control of the Hessian Continued Keyword Value Description irfo 0 Before using Hessian to update geometry modify it by sign flipping or reverting to an older Hessian 139 1 Before using Hessian to update geometry modify it by RFO rational function optimization level shifting 144 Default for geometry optimi zations that do not use dynamic constraints 2 Before using Hessian to update geometry modify it by P RFO parti tioned rational function optimization level shifting 144 Default for transition state searches Automatically set for geometry optimizations that use dynamic constraints In o
251. e jaguar command is jaguar command options where command is any of the commands listed in Table 10 1 The options may be given in any order and may precede any options specific to the command Jaguar 7 0 User Manual 263 Chapter 10 Running Jobs 264 Table 10 1 Commands for the jaguar command Command Description run version args runargs jobnames batch batch options script Jobnames pka jobname j2 jobname babel babel options nbo results options jobs jobnames jobids status all kill jobnames jobids status purge jobnames jobids stop jobnames jobids status machid platform scripts sysreq help Jaguar 7 0 User Manual Start the Jaguar jobs whose job names are listed using the speci fied version information and run time options Start a Jaguar batch job using the specified script The optional job names specify input files for the script See Section 10 2 on page 272 for more information on this command Start a Jaguar pK calculation Start a Jaguar J2 calculation Perform a file format conversion using Babel Run an NBO calculation Summarize results from the output file using the options speci fied See Section 5 1 on page 87 for more information on this command Show the status of the specified running Jaguar jobs or list the jobs that have the specified status The a11 option shows the sta tus of all jobs including completed
252. e new structure Finally the nuclear repulsion energy for the new geometry is listed If the molecular structure was not yet converged and the maximum number of geometry opti mization iterations allowed was not reached in the previous iteration the output from more geometry optimization iterations follow The output from each iteration begins with onee grid and rwr output in the usual formats and continues with output from scf which now starts with the calculation type and the energy output from each SCF iteration skipping the listed information about electrons orbitals and so on The output further continues with output in the usual formats from der1a rwr and der1b winding up with the output from geopt The last such geometry optimization iteration contains in the geopt output either the line Geometry optimization complete or the line stopping optimization maximum number of iterations reached depending on whether the convergence criteria were met before the maximum number of iterations was reached 5 3 5 Solvation 5 3 5 1 Output from a PBF Calculation Performing a solvation calculation involves several iterations in which the wave functions for the molecule in the gas phase are calculated The program ch performs electrostatic potential fitting which represents the wave function as a set of point charges on the atomic centers The interactions between the molecule and the solvent are evaluated by Jaguar s Poisson Bolt
253. e of 2 selects the pFON method You can use thermal smearing with the RHF ROHF UHF DFT RODFT and UDFT methods The number of alpha and beta electrons is kept the same during thermal smearing Thermal smearing can be used with or without symmetry and it can be used with the ipopsym keyword You can set the initial temperature using the fdtemp keyword The units of fdtemp are Kelvin The default initial temperature is 10 000 K The temperature decreases as a function of the rms density change When the density is close to the convergence threshold the temperature is set to zero The number of canonical orbitals kept in an SCF calculation is controlled by the cut20 keyword Eigenvectors of the overlap matrix i e canonical orbitals are discarded in a calcula tion if their eigenvalues are less than cut20 It may be necessary to fix the number of canonical orbitals during a calculation such as during a geometry optimization or scan or between calculations such as when comparing energies of related structures You can set the number of canonical orbitals with the ncanorb keyword and you can fix the number of canonical orbitals to the number determined for the initial structure by setting icanorb 1 When ncanorb is set to a value less than the number of basis functions the canonical orbitals with the lowest eigen values of the overlap matrix are discarded until there are ncanorb orbitals left Setting ncanorb sets icanorb to a positive value
254. e previous paragraph are important because they are each tested against the convergence criteria deter mined by the Convergence criteria setting in the Optimization tab as described in Section 4 1 on page 67 or alternatively the criteria set by the gconv keywords in the input file The criteria are described in detail in Section 8 5 10 on page 177 If the gradients are converged and the energy change is below 2 5 x 10 the optimization stops unless it is on the first geometry optimization iteration Similarly if the gradients are converged and one of the gradient criteria is 5 times lower than the convergence level then the optimization stops if the energy change is less than 2 5 x 10 Jaguar 7 0 User Manual 101 Chapter 5 Output 102 The symbol following each quantity used to judge convergence indicates how well converged it is The symbol 77 indicates convergence criteria that are not satisfied indicates criteria that are satisfied indicates criteria that are quite well satisfied essentially zero If the convergence criteria mentioned are not met and if the maximum epo indicates values that are number of iterations has not been exceeded the output notes molecular structure not yet converged and the optimization continues The output next lists the movement of the center of mass If the output option for the bond length and angles is enabled the output then lists this information for th
255. e resulting density p to yield a final DFT energy A more detailed description of density functional theory can be found in Refs 133 and 134 Jaguar 7 0 User Manual 153 154 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File This chapter describes the Jaguar input file and how to use it to run Jaguar from the command line You might want to run Jaguar from the command line in order to submit a job at a later time when computers are less busy to use batch scripts to run multiple jobs in succession to submit jobs from a non X terminal or to automate job submission with input files created by using other programs or by creating and editing input files yourself The sections in this chapter discuss the Jaguar input file format describing the general file format first then describing each section of the input file starting with the geometry input zmat and the keyword gen sections In the tables of this chapter default values of keywords are set in bold italic 8 1 General Description of the Input File The input file often begins with an optional line indicating the version number of Jaguar such as v60012 The other parts of the input file are either single lines composed of options in capital letters followed by arguments on the same line sections describing the molecule and the calculation whose formats will be described later in this chapter or comments 8 1 1 Input File Format The input file should have the f
256. e the basis set in the restart file to cc pWTZ f and restart the job See Section 6 5 on page 136 for a description of how to restart jobs This procedure will generally be significantly faster than running a GVB LMP2 cc pVTZ f job from scratch Jaguar 7 0 User Manual Chapter 3 Options 3 8 SCF Settings The SCF tab includes various settings that control the type of calculation and how the calcula tion is performed including the accuracy level the convergence method and criteria and the orbital symmetry and localization 3 8 1 Accuracy Level Jaguar can use integrals evaluated on a grid with the pseudospectral method and fully analytic integrals The grids used for various SCF iterations and the accuracy with which parts of the calculation are done greatly affect the timing and sometimes the accuracy of the entire calcu lation You can adjust the grids and the set of cutoff values determining these factors using the Accuracy level option menu For more information on grids and cutoffs see Section 9 4 on page 248 and Section 9 5 on page 252 The default Quick setting allows fast calculations to be performed using several different pseudospectral grid types and cutoffs that should generally produce well converged energies The Accurate setting which corresponds to tighter cutoffs and therefore somewhat slower calculations also uses a variety of pseudospectral grids If you choose the Ultrafine setting gt the cutoffs
257. e would appreciate it if you would describe them to us at the address given on page 322 preferably by e mailing us the input output and log files for the job with a brief explana tion To get converged results in the meantime you can try using level shifting and or set ting the accuracy level to Ultrafine both of which are described in Section 3 8 3 on page 47 and Section 3 8 1 on page 45 The calculation will be slower but convergence may be better for problem cases The settings available in the Start dialog box are not what you expected them to be Many of the options are determined by the schrodinger hosts file used for the job This file is the schrodinger hosts file found in the directory from which Maestro was started if it exists otherwise it is the schrodinger hosts file in your home directory if that file exists and if neither of those two files exists the default schrodinger hosts file for the submission host is used If you are using a different schrodinger hosts file from what you expect or if you are working with a new version of Jaguar and a new schrodinger hosts file has been installed on your computer you should examine the schrodinger hosts file for the job and make sure it is in the correct form and that the settings are appropriate See the Job Control Guide for a description of the schrodinger hosts file ee The job fails with a memory related error Memory fault out of memory or no memory avai
258. eal set of coordinates is one in which the energy change along each coordinate is maximized and the coupling between coordinates is mini mized The default coordinate system used by Jaguar is redundant internal coordinates In most cases this set of coordinates proves to be the most efficient There are cases where geometry optimizations with this set can fail One example is when a group of atoms becomes collinear and the internal coordinates become ill defined When this happens Jaguar chooses a new set of redundant internal coordinates If this process fails you can restart the optimization with a different choice of coordinates Jaguar provides two other coordinate systems which are available from the Coordinates option menu in the Optimization tab Cartesian and Z matrix gt Cartesian coordinates avoid the prob lems of collinear coordinate sets but an optimization in Cartesian coordinates is likely to take longer than one in redundant internal coordinates Using the Z matrix coordinates is the other alternative Choosing a set of Z matrix coordinates that produces an efficient optimization is not a trivial task and requires an understanding of the coupling between simple internal coor dinates You can mix Cartesian and Z matrix coordinates in the geometry definition zmat section but if you do you cannot use either of these two options for geometry optimizations 4 2 Constraining Coordinates When you optimize the geometry of
259. ecify the display with the following command substituting the name of your X server or terminal for displayhost csh tesh setenv DISPLAY displayhost 0 0 sh bash ksh export DISPLAY displayhost 0 0 The error message Xlib connection to displayhost 0 0 refused by server Xlib Client is not authorized to connect to Server Error Can t Open display usually means one of two things First if you are not the person who initially logged on to the X server you cannot bring up any type of X window on the display In this case you should log out and log in as yourself Second if your X server and the host from which you start Maestro the launch host are not the same machine the X server might not recognize the right of that host to display To correct this problem type the following in a window on your X server xauth nextract displayhost 0 0 rsh ihost xauth nmerge Here ihost should be replaced by the name of the launch host Also the remote shell command should be used for rsh usually bin ucb rsh serves this purpose but rsh gives usr bin remsh on some machines If the restricted shell rsh precedes the remote shell version in your path you must use the full path name If the xauth command listed above results in the message xauth Command not found your path probably does not include usr bin X11 and you should include usr bin X11 in your path You could also substitute usr bin X11 xauth for xauth in the c
260. efault criteria are multiplied by a factor of three and a higher priority is given to the energy convergence criterion Thus if the energy change criterion is met before the gradient and displacement criteria have been met the geometry is considered converged See Section 8 5 10 on page 177 for details on the geometry optimization conver gence criteria or information on how to edit the input file to set them directly In case the optimization process does not converge you can set an upper limit on the number of steps taken by entering a value in the Maximum steps text box The default is 100 Many cases will meet the convergence criteria after ten or fewer geometries are computed However input containing very floppy molecules transition metal complexes poor initial geometries or poor initial Hessians may require many more cycles and in particularly bad cases may also require you to stop the calculation and restart it with a change in one or more of the other default settings described below 4 1 2 The Initial Hessian To perform an optimization Jaguar first needs to read or generate an initial Hessian second derivative matrix or force constant matrix The Hessian and the gradient are used to define a search direction that should result in a lowering of the energy You can provide Jaguar with a Hessian in the hess section of an input file as described in Section 8 9 on page 228 For instance if you restart a geometry optimization from
261. el choose Selected entries from the Use structures from option menu Jaguar s default calculation settings B3LYP 6 31G are appropriate for refining the struc tures of conformers so at this point you can simply click the Start button and launch your job If the host or queue on which you want to run the job has as many CPUs available as there are Jaguar 7 0 User Manual Chapter 6 Using Jaguar conformers and you have sufficient license tokens you can set the number of CPUs to the number of conformers All conformers are optimized at the same time on separate processors for maximum efficiency When the Jaguar optimization results are incorporated into the project you can use the Macro Model redundant conformer elimination tool to remove any duplicate structures in case some of the conformers that appeared to be different at the MM level were refined to the same struc ture at the QM level See Chapter 18 of the MacroModel User Manual for more information on this tool 6 7 Generating Input Files for GAUSSIAN We recognize that some Jaguar users also use GAUSSIAN for calculations Therefore Jaguar can generate or read GAUSSIAN input files If you plan to perform GVB calculations with GAUSSIAN you may find this feature particularly useful since you can use Jaguar to generate a high quality GVB initial guess automatically You can use the GUI as a convenient tool to create GAUSSIAN input files The output file that is produced fr
262. elated to Your Temporary Directory eesssssss 286 11 1 5 Problems Running Jaguar Calculations on Other Nodes 287 11 2 Other Proble Suninn reet tetro dira erbe te EE SH E eH DE QUEE SPP NUI Idea fo 288 Chapter 12 Parallel Jaca usan nodi dx REV MCA ULP UE RR E 291 12 1 Installing Parallel Jaguar 291 12 1 1 SGI IRIX mips4 and SGI Linux ia64 Altix Installations 292 12 1 2 Linux x86 and Linux ia64 non Altix Installations essessss 293 12 1 2 1 Installing MPICH 12 1 2 2 Gonfiguretlon Gotta tutta duced icta am incolis idu i suf e Jaguar 7 0 User Manual Contents 12 1 2 3 Launching the Secure Gervers AEN 296 12 1 2 4 Selecting Nodes for VOD issessecssscsssscsgescstestsstacesasgecassaycesends seceigenscaciacs 299 12 1 2 5 Troubleshooting Parallel Job Problems esee 299 121 3 IBM Installation ocn reri red rt pip Pei PU IE FORE ee Lb REED PETERE EPOR ies 300 12 2 Running Jobs in Parallel 301 Chapter 13 The pK Prediction Module 303 13 1 Theory of pK Calculation nri ete riens 304 13 1 1 Ab initio Quantum Chemical Calculation of pK Values 304 13 422 eelere e EE 306 13 2 Predicting pK Values in Complex Systems esses 307 13 2 1 Gontormational F exibility iiid e RA ede HAE BER RATE MMMEPR AT AM MES 307 13 2
263. eld R Pople J A J Chem Phys 1972 56 2257 Francl M M Pietro W J Hehre W J Binkley J S Gordon M S DeFrees D J Pople J A J Chem Phys 1982 77 3654 Rassolov V A Pople J A Ratner M A Windus T L J Chem Phys 1998 109 1223 Clark T Chandrasekhar J Spitznagel G W Schleyer P von R J Comput Chem 1983 4 294 Frisch M J Pople J A Binkley J S J Chem Phys 1984 80 3265 Krishnan R Binkley J S Seeger R Pople J A J Chem Phys 1980 72 650 McLean A D Chandler G S J Chem Phys 1980 72 5639 Mitin A V Baker J Pulay P J Chem Phys 2003 116 7775 Dunning T H Jr Hay P J Chapter 1 in Modern Theoretical Chemistry Methods of Electronic Structure Theory Schaefer H F III Ed Plenum New York 1977 Vol 3 Rapp A K Goddard W A Unpublished work Dunning T H Jr J Chem Phys 1989 90 1007 Kendall R A Dunning T H Jr Harrison R J J Chem Phys 1992 96 6796 Woon D E Dunning T H Jr J Chem Phys 1993 98 1358 Woon D E Dunning T H Jr J Chem Phys 1994 100 2975 Jaguar 7 0 User Manual References 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 Easton R E Giesen D J Welch A Cramer C J Truhlar D G Theor Chim Acta 1996 93 281 Thompson J D
264. ell volume which is the volume between the spheres whose radii are the average of the current and previous shell radii and the current and following shell radii After the flag for the grid information for each atomic grid is provided The first line of each atomic grid section contains two integers one providing the atomic number for that atom and the other giving the number of shells to be described Currently this second number should be 30 or less The next line contains that number of entries defining the radial shell spacing listing the radius of each shell in bohr Grid points for that shell will be placed at that radius in a pattern determined by the integers given in the third line This last line of integers represents the density of the angular grid for each shell The values are explained below The default grid file for Jaguar version 7 0 begins as follows gridv0220 5 24 Jaguar 7 0 User Manual 249 Chapter 9 Other Jaguar Files 250 BASIS 6 31G coarse grid 1 ce N Ww cy N nd 0 71955 1 74518 2 82595 3 94135 6 40743 il ps LA N W 20699 0 45860 0 97184 1 61794 2 40119 3 26487 5 20964 379731 59584 1 69094 3 39571 5 30494 7 49262 11 30338 16 61803 349 T al o ed ta e bh Blank lines have been added between atomic grids for readability Data may be spread over multiple lines As explained above the beginning of the default grid file indicates that five grid types are listed for
265. en you select Structure in this dialog box the three structures are available in separate tabs labeled Reactant Product and Transi tion State If you want to use the same Z matrix for all geometries choose Standardize Z matrix format from the Structures menu You can then set any variables to the desired values If you want to apply constraints in the search you must add them to the main geometry The main geometry for the job is the topmost in the Structures section the transition state for stan dard and QST searches and the reactant for LST searches To add constraints click the inclu sion button for the main geometry then add the constraints in the Optimization tab see Section 4 2 on page 70 4 3 3 Searching Along a Particular Hessian Eigenvector If you are using the standard non QST guided transition state optimization method you can specify a Hessian eigenvector for the optimizer to follow The choices of eigenvector are avail able from the Search along option menu Lowest Hessian eigenvector the default the Lowest non torsional mode the Lowest bond stretch mode or a User selected eigen vector You also have access to these search directions if you are doing an LST search in addition to the Reactant product path Under certain circumstances you might want to direct your transition state search using these options rather than having the optimizer simply minimize along the lowest Hessian eigen vector fo
266. ence Try the sample calculation in Section 2 1 to get some experience running Jaguar and to make sure your system is set up properly If you have problems starting or using Maestro or performing the calculation you may be able to solve them using the troubleshooting sugges tions in Chapter 11 If any problems persist contact your system manager or Schrodinger The rest of this chapter describes the basics of running Jaguar from Maestro including entering a geometry and submitting a job Jaguar has a wide range of options for different kinds of calculations Setting these from Maestro is described in Chapter 3 Jaguar can perform many kinds of calculations such as geometry optimizations transition state searches and various coordinate scans Setting up these calculations is described in Chapter 4 Jaguar also provides special capabilities for pK prediction and accurate calculations with J2 theory J2 theory calculations are described in this chapter pK calculations are described in Chapter 13 The footnotes describe Jaguar input file keywords and sections that correspond to particular GUI settings If you are working from Maestro you can ignore these footnotes but you may later find them helpful if you decide to use input files to submit jobs without using Maestro or if you want to edit keywords directly using the Edit Job dialog box 2 14 Sample Calculation This section provides instructions for running a sample calculation on the wate
267. energy breakdown for the scf output also describes the electron nuclear and kinetic contri butions to the total one electron terms in the energy as well as the virial ratio NIT where V is the potential energy and T is the kinetic energy This ratio should be 2 if the calculation satis fies the virial theorem After the first sc output the output from the first run of the program ch appears Since performing a solvation calculation enables electrostatic potential fitting to atomic centers the usual output for that option which is described in Section 5 3 7 on page 109 is included every time output from the program ch appears in the output file The post program writes out the necessary input files for the Poisson Boltzmann solver this step is noted in the output file The next output section comes from the Poisson Boltzmann solver The output includes infor mation on the area in of the molecular surface formed from the intersection of spheres with the van der Waals radii centered on the various atoms the reaction field energy in kT where T 298 K which is the energy of the interaction of the atom centered charges with the solvent the solvent accessible surface area in A which reflects the surface formed from the points whose closest distance from the molecular surface is equal to the probe radius of the solvent and the cavity energy in kT which is computed to be the solvation energy of a nonpolar solute whose size and shape
268. energy from the job RuCp2 and the second lists the final energy from the job piperidine If you use the option title the table has column headings indicating the type of information listed The columns appear in the table in the same order they are listed in the jaguar results command For instance the command jaguar results title jobname method energy bio out A h20 b3lyp out where bio out and bio b3lyp out are output files from jobs at the Hartree Fock and B3LYP density functional theory levels respectively gives the table Jobname Method Energy hartree bio HF 76 023641 bio b3lyp B3LYP 76 418721 with the job name method and energy listed from left to right in the same order they were in the jaguar results command If you want to see ahead of time what the column headings of your table would look like without any results listed use the titleonly option The Jaguar results tables can list both information describing the job run for instance its name the basis set and SCF method used or the stoichiometry of the molecule and informa tion about the results of the job for example the final energy or dipole moment Each of these types of information appears in a column in the table 5 1 2 Reporting Intermediate Results By default only the final results are reported for each job therefore for instance a table of results from three jobs would have three rows of information However you can also request that infor
269. ents as e15 6 in table Examples of each of these style options appear below In the first option listed the phrase large elements indicates that only coefficients larger than a particular value generally 05 are listed The notations f5 2 and the like refer to standard Fortran formats The word labels indicates that the atom identifiers for instance h2 and the basis function types for instance S for s Z for p or XX for d are shown Note that in canonical orbital space the labels indicating atom identifiers and basis function types are meaningless The output for each style is shown in either table form or list form When the orbital output is in table form each function s coefficient for each orbital is shown with the functions shown in numbered rows and the orbitals in numbered columns When it is in list form each orbital is listed in turn with the basis function coefficients listed in order For the third and fourth options those with f19 15 and f8 5 formatting all coefficients are listed in order but without numbering The three styles presented in list form also include information on the occupation and energy of each orbital If you generate output in the f19 15 or f8 5 formats you can use it for input in the guess section of an input file which is described in detail in Section 8 10 on page 229 or for input to GAUS SIAN guess cards 23 This setting corresponds to having all of the orbital
270. enu of the Applications menu in the main window You can set optimization parameters that are not unique to transition state searches in the Optimization tab The Transition state tab contains controls for settings that are specific to transition state searches including selection of the reactant and product geometries 16 Keyword igeopt 2 in the gen section Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans This section describes various transition state search options For information on general settings that are useful for all types of geometry optimizations see Section 4 1 on page 67 4 3 1 Transition State Search Method The first choice listed in the Transition State tab is the Search method which can be set to Standard LST 5 or QST 8 The default choice is Standard because it does not require more than one input geometry but if you can provide product and reactant geometries we recom mend selecting LST If you also have a good guess for the transition state select QST Both the LST option and the QST option set up a QST guided search If you select LST Jaguar generates a transition state guess by interpolating between the reactant and product geome tries By default this linear synchronous transit LST transition state guess is midway between the reactant and product geometries This choice is indicated by the default value of 0 5 for the Initial LST guess setting To pick a transition state guess closer t
271. er Manual 127 Chapter 5 Output 128 For the Format option All elements as f8 5 in list 1 Orbital Energy 20 555133 Occupation 1 000000 Symmetry A1 0 99466 0 02122 0 00000 0 00000 0 00155 0 00430 0 00000 0 00000 0 00019 0 00395 0 00376 0 00381 0 00000 0 00000 0 00000 0 00000 0 00034 0 00000 0 00037 0 00025 0 00000 0 00034 0 00000 0 00037 0 00025 2 Orbital Energy 1 345597 Occupation 1 000000 Symmetry A1 0 21055 0 47102 0 00000 0 00000 0 08586 0 41777 0 00000 0 00000 0 03150 0 00141 0 00617 0 00819 0 00000 0 00000 0 00000 0 14851 0 01307 0 00000 0 02205 0 01342 0 14851 0 01307 0 00000 0 02205 0 01342 Ls For the Format option All elements as e15 6 in table 1 2 3 1 9 946611E 01 2 105494E 01 s scs 2 2 122377E 02 4 710188E 01 5 1 550432E 03 8 586249E 02 6 4 301783E 03 4 177747E 01 QUU ee 1 485137E 01 2 Lee ES 1 485137E 01 ee 1 341957E 02 5 7 The Log File The log file an output file which appears in the local job directory provides information on the progress of a run The current contents of a job s log file is displayed in the Monitor panel The log file notes when each program within Jaguar is complete as well as noting data from each SCF iteration The data from the SCF iterations is shown in table form Some of the text for the column headings should be read down rather than across For the table of SCF iteration information the number of the iteration is provided first in each row followed by
272. er of contracted dealiasing functions In the sample file the first atom whose dealiasing functions are listed is hydrogen since the atomic number listed is 1 The same line says that ten uncontracted functions and two contracted functions will be specified for each range in the five sets of dealiasing functions for hydrogen characters indi The second line for the same atom type should list real dealiasing exponents for each uncon tracted function The exponents specify what functions can be used For instance in the sample file hydrogen s s type uncontracted basis function from the first exponent would be N e 0406347 While the p type uncontracted basis function for the same exponent would be Nre 0406347 N and N are normalization constants Below those two lines the dealiasing function sets for that atom type should be listed set by set By default the first set will be used for the coarse grid the second for the medium grid and so on with the last set corresponding to the gradient This ordering can be changed in the gen section of the input file Each set should contain a line for each neighbor range the long range functions should be specified first then the home atom functions then the functions for each neighbor range in increasing order Within each line there should be several integers one for each uncontracted function then one for each contracted function These integers dictate how to construct the actual functio
273. erations is less than this value the density is converged For polarizability and hyperpo larizability calculations if the energy convergence criterion described in the previous para graph is satisfied first the calculation ends even if the RMS density matrix element change criterion has not been met and vice versa 3 8 3 Convergence Methods Jaguar provides a range of options for controlling the convergence of SCF calculations These options are available in the Convergence methods section Level shifting adds a constant to the diagonal of the Fock matrix for the virtual orbitals before diagonalization This reduces the mixing of the occupied and virtual orbitals and damps the changes in the orbitals As a result the convergence is slower but this method often helps otherwise intractable cases to converge Level shifting is normally varied during the course of an SCF calculation without having to explicitly set a value Useful SCF level shift values are generally in the range 0 3 1 0 You can set the constant in the SCF Level shift text box Thermal smearing populates the virtual orbitals using a Fermi Dirac distribution with a given temperature allowing orbitals other than the default orbitals to be populated The temperature is progressively reduced so that the true occupied orbitals are the only ones populated at the end of the calculation This procedure makes it easier for orbitals to switch if they are not in the default initial gue
274. es various frequency related proper ties can also be computed by setting the appropriate keywords Most of these keywords which are listed in Table 8 26 correspond to GUI options described in Section 3 11 on page 58 Only the values listed in the table are allowed Table 8 26 Keywords for frequency related properties Keyword Value Description ifreq 0 Do not calculate frequencies second derivatives 1 Get frequencies from Hessian of second derivatives of energy 1 Calculate frequencies from most recent Hessian from end of optimi zation or from initial Hessian if initial Hessian was never updated maxitcp 35 Maximum number of CPHF iterations rmscp 5x10 CPHF convergence threshold imw 0 Print normal modes in cartesian coordinates without mass weighting 1 Print normal modes in mass weighted cartesian coordinates isqm 0 Do not scale frequencies using Pulay s Modified Scaled Quantum Mechanical Force Fields SQM method 1 Scale frequencies using Pulay s SQM method and use scaled frequen cies for thermochemical calculations only allowed for B3LYP calcu lations with the 6 31G basis set scalfr gt 0 Scale vibrational frequencies by this factor default is 1 0 and use scaled frequencies for thermochemical calculations irder 0 Do not compute dipole derivatives or IR intensities for vibrational fre quencies 1 Compute derivatives of dipole moment and IR intensities for vibra tional frequencies see text for detai
275. es on non Altix machines Whether you have an x86 machine or an ia64 machine you may need to compile Jaguar s MPI compatibility libraries against your own MPI installation in the following circumstances 2 Please see the notice regarding third party programs and third party Web sites on the copyright page at the front of this manual Jaguar 7 0 User Manual 293 Chapter 12 Parallel Jaguar 294 You intend to run Jaguar on a cluster that uses high speed network switches such as Giga bitEthernet or Myrinet You have a specially tuned MPI library or one that is based on the MPI 2 standard The launcher for your MPI distribution is not called mpirun To do so unpack the schrodinger_mpi tar gz file referred to above and follow the instructions in the README provided in it If you want to use MPICH 1 but have not installed it yet follow the instructions below 12 1 2 1 Installing MPICH The instructions for building MPICH in this section are for the version that is based on the MPI 1 standard which can be found at http www unix mcs anl gov mpi mpich1 MPICH based on the MPI 2 standard can also be found at this same website but in order to use it you must compile Jaguar s MPI compatibility libraries as described above Detailed instructions for building installing and testing MPICH are included with the MPICH source code When you build MPICH from the source code include the following configure
276. ess either basis set uses effective core potentials If you suspect that the initial guess is leading to the wrong state you can run a calculation with the initial guess only by choosing Initial Guess Only from the Jaguar submenu of the Applica tions menu or setting igonly 1 You can then examine the orbitals in the output If you also generate orbitals surfaces in the Properties tab see Section 3 12 on page 63 you can examine the orbitals in Maestro to see if they are what you expect If the occupied orbitals are not correct you can swap them by including an orbman section in the input file see Section 8 14 on page 232 for more information When you swap orbitals you might also want to fix the orbital populations in each symmetry by selecting Fixed symmetry populations in the SCF tab or setting ipopsym 1 By default populations in each symmetry are allowed to vary so that if the default initial guess is incorrect there is a chance of converging to the correct state Of course you must use symmetry for this strategy to be effective 6 1 2 GVB Initial Guess For GVB calculations the GVB initial guess is automatically constructed from the Hartree Fock initial guess by piecewise localization Another option is to use a converged HF wave function as the basis for the GVB initial guess Because this choice requires two SCF calcula tions one for HF and one for GVB it is considerably more expensive than using the GVB initial gue
277. ettings This keyword can help when pseudospectral error is particularly high but it works by removing more eigenvectors from the overlap matrix This effectively reduces the size of the basis set which means that if you want to compare energies for two differ ent molecules you need to use the same value for iacscf You might need to increase the setting of maxit to 100 or more when using this keyword 6 3 Geometry Optimization If you have built a structure in Maestro or suspect that the structure is not very close to the optimized geometry it can be useful to perform a geometry cleanup To clean up a geometry in Maestro using molecular mechanics with a universal force field UFF available for all elements click the Geometry Cleanup button in the Build panel For flexible molecules which might adopt one of several possible conformations you might consider performing a conformational search with MacroModel See Chapter 9 of the Macro Model User Manual for more information If you are performing a geometry optimization and are not starting from a high quality initial molecular structure you might want to do a quick and dirty calculation to obtain a somewhat better geometry then perform a more accurate calculation by starting with the results you have generated already For example if you wanted to perform an LMP2 geometry optimization Jaguar 7 0 User Manual 135 Chapter 6 Using Jaguar 136 you could start by per
278. ey can be use as Jaguar input files All but the first file contain the END OF INPUT string which Jaguar treats as a comment See the UNIX man page for csplit for more information man csplit For one and two dimensional scans Jaguar writes grd files which can be read by Maestro and displayed in the 1D Plot and 2D Plot panels These panels display interactive plots and contour plots respectively For more information on these panels see Section 8 3 of the MacroModel User Manual The panels were originally designed for the display of dihedral angle scans for MacroModel You can use any kind of scan except at scans i e scans that supply a list of coordinate values If you generated surfaces in the scan job the surfaces are incorporated along with the struc tures at each point 4 5 Intrinsic Reaction Coordinate Calculations Intrinsic Reaction Coordinate IRC calculations can be used to check that the given transition state is the expected transition state for the reaction of interest IRC calculations start at a tran sition state and move downhill in energy along the reaction path toward a minimum of the potential energy surface calculating a series of points in which all geometric variables orthog onal to the path are optimized IRC scans have been implemented in Jaguar using the methods described in Ref 178 The implementation includes both IRC and minimum energy path MEP calculations The differ ence between the two is that the
279. f 30 takes 5 steps 0 30 60 90 and 120 As an example to vary the angle HCCH over the values 0 30 60 90 120 150 180 you could use any one of the following lines HCCH from 0 to 180 by 30 HCCH 0 to 180 in 7 HCCH from 0 by 30 in 7 You can also set a coordinate to a set of specific values using the word at With this format the values of the scanned coordinate do not have to be evenly spaced For example this line would vary the angle HCCH over the values 0 30 60 70 80 90 120 150 HCCH at 0 30 60 70 80 90 120 150 You can define up to five scan coordinates at once The first scan coordinate will be in the innermost loop that is the scanner will run through all values of the first scan coordinate before updating the others and so on finally looping last over the last scan coordinate Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans For each geometry in the scan the default initial guess for the wave function and the default initial Hessian are taken from the previous geometry You can change this behavior using the scanguess and scanhess keywords in the gen section of the input file 4 4 3 Constraining Coordinates for Torsional Scans In most cases more than one set of atoms can be used to define a torsional angle This means that if you want to scan a torsional angle the torsional profile may depend upon the particular set of atoms chosen to represent the torsional angle since the sca
280. f iterations 69 136 178 output description eene 100 output of Torees 99 output options eeeeeeeenenrnr 122 refinement of initial Hessian for 16 78 80 159 160 180 GI 135 136 troubleshooting eee 289 trust radius for 181 182 186 updating of Hessian during 180 see also transition state optimization geometry SCANS inie asorti 80 84 geometry translation and rotation of during calculation ecce re ett retten 92 geopt program orte 234 pu M 100 Jaguar 7 0 User Manual 337 Index 338 ghost atOms iterat ror egi edet 15 use in charge fitting to bond midpoints 110 Gibbs free energy calculations 62 63 115 191 gradient see analytic gradient of energy Grasp program eeseeseeseeennenenrennennennne 189 grid and RwR information output keyword 205 grid file default aea chen 237 description and format 248 250 specifying in input file 155 grid ptOgram as siet nennt teoria 233 output from eeeenee 94 100 102 grid shell locations keyword for output of 204 BS 68 156 212 for electrostatic potential fitting 54 188 212 grid file eoi tera tese 155 information in log file 129 information in output sss 94 96
281. fferent versions of this information for LMP2 calculations than it does for other wave function types Therefore the first non blank line of the file should begin CALCULATION TYPE 01 with any comment allowed after this string indicating that the information following that line 1s for HF DFT or GVB wave functions After all the information in the file for these calcula tions the file should contain this line CALCULATION TYPE 02 followed by information for LMP2 wave functions 9 6 1 Describing Bonding Types in the Lewis File The bonding type information for HF DFT or GVB wave functions should follow the first line describing the calculation type The first line of this information should begin BONDING TYPE 01 and the rest of the bonding type information should not contain any blank lines except the last line which signals the end of bonding type information Bonding type information should be listed for each relevant element in turn The information for the first atom should follow immediately after the BONDING TYPE 01 label The first char Jaguar 7 0 User Manual 255 Chapter 9 Other Jaguar Files 256 acter of the information for that atom should begin with the atom s atomic number The following lines should describe up to five groups of bonds for that atom Each group must begin with the word Group with no leading spaces and must contain information for bond orders 1 2 and 3 with
282. fgrdX pqq 66 39 66 where X is m f g u d or c signifying medium fine gradient ultrafine second derivatives and CPHF and correspond to grids 10 11 12 13 8 and 9 nr is the number of radial shells na is the angular grid entry number from Table 9 1 p is a number denoting the radial shell distribution scheme and qq is a two digit number denoting the pruning scheme The possible values for p are 1 geometric distribution 174 the default for medium fine and gradient grids 2 Becke s Gauss Chebyshev distribution 175 3 described in ref 176 and 4 the Mura Knowles distribution 177 the default for the Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File ultrafine second derivative CPHF and grid 14 The values of qq can be 00 11 22 or 33 00 is the default for the medium grid 11 is the default for the fine and gradient grids and 33 is the default for the second derivative CPHF and ultrafine grids 22 turns off pruning The value for ndfgrdX2 is interpreted as an offset to be added to the angular value for each radial shell that is determined from the pruning scheme You can get more information about both pseudospectral and DFT grids for a job by setting ip23 2 in the input file Table 8 37 shows the types of grids that can be specified for portions of the calculation that do not involve density functional theory Generally these grid type
283. ficient is being evaluated is to be approx imated by short range dealiasing functions then the dealiasing functions for first order neigh bors will be used for each atom within this distance of the atom upon which the basis function is centered except for the basis function atom itself for which the home atom dealiasing func tions will be used The second distance defines which atoms are considered second order neighbors to each other and so on Since the number of neighbor ranges includes not only these ranges but also the long range over the entire molecule and the home atom range consisting of the relevant atom itself the number of neighbor ranges actually specified in this line of the daf file should be two less than the number of ranges listed in the previous line Thus in the sample file the distances listed specify the neighbor ranges for first through fourth order neighbors The rest of the daf file contains the dealiasing function sets for each atom type within each basis set The data for each basis set should begin with a line listing the basis set name as listed in Table 3 1 on page 32 and Table 3 2 on page 34 including the cating the polarization functions e g 6 31G The first line for each atom type for that basis set should list three integers the atomic number for that atom type the number of uncontracted dealiasing functions about to be listed for each neighbor range in each set and the corre sponding numb
284. file is read from the current working directory 2 Any options that are defined are applied to the contents of the template file Options that are given on the job specification line override options that are specified with an OPTIONS directive Option syntax is given below 3 A new input file new name in is created The new file is written to the directory specified by a WORKDIR directive or if no WORKDIR directive has been given to the current working directory If new name is not specified new name is set to template name 1f the file new name in already exists it is overwrit ten unless you use the r option described later in this section 4 The Jaguar job is run using jaguar run with this new file as input The command line options for the Jaguar job are specified by the FLAGS directive Tem porary files generated during the job are written to the subdirectory new name in the scratch directory and output files are written to the directory listed on the OUTDIR line if given or from the current working directory The template job name can either be the stem of an existing input file or the string JOB If the string JOB is used the batch script is run multiple times substituting for JOB the job names that are provided as arguments to the jaguar batch command For example for the job speci fication h2o bio dft dftname b3 lyp the file h20 in is read the keyword setting d tname b31yp is added to the gen section of
285. files for jobs 6 and 7 the atoms of one fragment must be marked as counterpoise atoms also called ghost atoms so that only their basis functions are used In Jaguar a coun terpoise atom is indicated by appending a to the atom label For example to calculate the interaction energy of a water molecule with a methanol molecule the zmat section for one counterpoise job would have the atoms of for methanol marked as counterpoise atoms amp zmat 01e 0 3380316687 0 9068671477 0 0000000000 H2 0 3206434752 0 0520359937 0 0000000000 c3e 0 9752459717 1 3666159794 0 0000000000 H4 0 9478196867 2 4513855069 0 0000000000 H5 1 5357440779 1 0497731323 0 8817844743 H6 1 5357440779 1 0497731323 0 8817844743 07 0 4959747210 1 9447535985 0 0000000000 H8 1 0372322234 2 1494734847 0 7574958845 H9 1 0372322234 2 1494734847 0 7574958845 amp In the other counterpoise job the zmat section would have the atoms of the water molecule marked as counterpoise atoms amp zmat O1 0 3380316687 0 9068671477 0 0000000000 H2 0 3206434752 0 0520359937 0 0000000000 C3 0 9752459717 1 3666159794 0 0000000000 H4 0 9478196867 2 4513855069 0 0000000000 H5 1 5357440779 1 0497731323 0 8817844743 H6 1 5357440779 1 0497731323 0 8817844743 o7 0 4959747210 1 9447535985 0 0000000000 H8 1 0372322234 2 1494734847 0 7574958845 H9 1 0372322234 2 1494734847 0 7574958845 amp You can also indicate counterpoise atoms in an atomic section
286. fine grid compute Q on the fly in the program scf 1 For ultrafine grid compute Q in the program rwr and store on disk for later use iqgrad 0 For gradient grid compute Q on the fly in the program scf 1 For gradient grid compute Q in the program rwr and store on disk for later use iqlmp2 0 For LMP2 grid compute Q on the fly in the program scf 1 For LMP2 grid compute Q in the program rwr and store on disk for later use iqlImp2grad 0 For LMP2 gradient grid compute Q on the fly in the program scf 1 For LMP2 gradient grid compute Q in the program rwr and store on disk for later use 8 5 27 Plotting Keywords You can generate a plot file using keywords in the gen section that contains the values of the density the spin density the electrostatic potential or orbital amplitudes The data values are tabulated on a rectangular grid the box which is generated automatically and encompasses the van der Waals radii of all atoms in the molecule The plot file can be used by Maestro and other programs to display surfaces for a particular value of the density potential or amplitude The length units for the grid are set with the iunit keyword The possible values of the plotting keywords are given in Table 8 41 See Section 3 12 on page 63 for information on setting up plot data using the GUI Orbital amplitude data can only be generated for SCF and GVB wave functions MP2 calcula tions do not generate natural orbitals
287. followed by the same character string Nested loops are also allowed The following path illustrates a loop which will cause the programs pre onee grid and ig to run once the series of programs rwr scf derla rwr der1b and geopt to run until the conver gence criteria for geometry optimization are satisfied and the program post to run once amp path pre onee grid hfig loopal rwr scf derla rwr derlb geopt gotoal post amp If you put a jump label between a loop label and a goto label where jump is followed by the same character string that follows loop and goto jumpa1 for the above path for instance the path will jump to the end of the loop after the goto label and will exit the loop when the jump label indicates that the convergence criterion for that program is reached Note that since loops only exit when convergence is reached the program before a goto or jump label must have such a criterion The three programs that can precede a goto or jump label are sc when it is being used for solvation runs geopt and nude Sometimes you might want a path to include a command of more than one word for instance you might want to use the UNIX command mv old filename new filename to rename a file In that case you can enter the path section in such a way that each line contains a single command To enter the path this way you must include the word line after the amp path or path label at the beginning of the path section 8 17 N
288. for LMP2 wave functions Moments are computed with respect to the center of mass of the molecule Note that LMP2 dipole moments can be computationally expensive since computing them accurately requires coupled perturbed Hartree Fock calculations By default all moments are calculated You can restrict the order of the moments with the keyword ldips in the gen section If you select one of the higher order moments all moments of lower order are also calculated If atomic charges are computed either by fitting of the elec trostatic potential 70 71 or by Mulliken population analysis 73 the multipole moments are also calculated from these point charges for comparison The dipole moment and its cartesian components are written to the output structure file mae and incorporated as properties in the Project Table It can be displayed in the Workspace by choosing Dipole Moment from the Display menu The dipole moment is displayed as a lilac arrow pointing from negative to positive with the base of the arrow at the coordinate origin 3 10 4 Natural Bond Orbital NBO Analysis When you select NBO analysis a default Natural Bond Orbital NBO analysis is performed at the end of the Jaguar job The output from the NBO analysis is included in the Jaguar output file Other options for NBO calculations can also be specified in the nbo section or in the core choose and nrtstr sections of the Jaguar input file It is not possible to run NEDA Natural
289. for idft If jdft2 1 you can set up a customized functional using the keywords yhf yexl1 yexl9 yexnln ycorln and ycornln which correspond to the keywords in Table 8 15 e g xexl1 If you do a post SCF DFT energy evaluation you should not perform a geometry optimization or calculate the solvation energy polarizability or any other properties Table 8 15 Functional coefficient keywords Keyword Corresponding Functional or Exact Exchange xhf exact exchange Hartree Fock xexl1 Slater local exchange functional xexl9 Xa local exchange functional xexnil Becke 1988 nonlocal gradient correction to exchange xexnl3 Becke 1998 B98 local and nonlocal exchange functional xexnl4 Perdew Wang GGA II 1991 nonlocal exchange functional xexnl6 Schmider and Becke 1998 SB98 local and nonlocal exchange functional xexnl7 HCTH407 local and nonlocal exchange functional xexnl8 B97 local and nonlocal exchange functional xexnl9 PBE local and nonlocal exchange functional xexnl11 Perdew Wang 1991 exchange as modified by Adamo and Barone mPW xexnl12 mPW as modified by Zhao and Truhlar for PWB6K xexnl13 mPW as modified by Zhao and Truhlar for PW6B95 xexnl14 M05 local and non local exchange functional xexnl15 M05 2X local and non local exchange functional xcorl1 VWN local correlation functional xcorl2 VWNS local correlation functional xcorl3 Perdew Zunger 1981 local correlation functional xcorl4 Perdew Wang GGA II 1991 local correla
290. for the specified job and kills all instances of the job with the name jobname To kill a specific job use the job ID which is unique instead of the job name You cannot kill stranded jobs with jaguar kill because the job control facility does not have the necessary information about those jobs Jaguar 7 0 User Manual Chapter 10 Running Jobs 10 1 5 Converting File Formats Jaguar uses the Babel program 26 to convert between many of the file formats used in computational chemistry Babel can read over 40 kinds of input and output file types and writes both cartesian and Z matrix geometry specifications Babel is used in the GUI to read and write files that are not in Jaguar or Maestro format You can also request Jaguar to write out files during a job run using the babel or babelg keywords see Section 8 5 20 on page 201 for more information To convert file formats from the command line you can use the jaguar babel command The syntax of the command is jaguar babel v iinput format input file h d range ooutput format output file split The i and o arguments are required to set the input and output formats respectively The output format keywords are listed in Table 8 31 on page 202 the input format keywords are listed in Table 10 3 Note that the format keywords are not used for file extensions as they are when you use the babel and babelg keywords in a Jaguar input file The input and output file names given
291. for these calculations and the symmetry labels are not included in the output of orbital energies The program loclmp2 which computes localized orbitals runs after scf in an LMP2 calcula tion and its output notes the number of orbitals that are localized Below that output the output from the program 1mp2 appears For local MP2 calculations the output begins by listing the localized orbitals involved in the local MP2 treatment namely the localized orbitals centered on one or both atoms in the pairs of atoms for which an LMP2 level treatment was requested All LMP2 output includes a description of the type of orbitals used in the MP2 calculation First it lists the total number of orbitals Next it lists the number of frozen core and valence MP2 orbitals The numbers of core and valence orbitals will be affected by whether you use valence electrons only or all electrons for the atoms in the calculation Next the numbers of occupied and virtual orbitals for the molecule are listed The list ends with the number of exchange Hamiltonians Jaguar 7 0 User Manual 97 Chapter 5 Output 98 Some information on the convergence of the LMP2 energy correction appears below the list of orbital information followed by the Hartree Fock energy and the LMP2 energy correction which gives the improvement to the energy over the HF value The total LMP2 energy the HF energy plus the correction is given immediately afterwards If your job
292. forming a Hartree Fock geometry optimization then restart the calcula tion using the HF results in an LMP2 geometry optimization See Section 6 5 for a description of restarting calculations and incorporating previous results in a later run Whenever you are doing a geometry optimization make sure that you really do obtain a converged structure the run ends before converging if you reach the maximum number of iter ations allowed as set in the Optimization tab If it did not reach convergence you can restart the run as described in Section 6 5 6 4 Setting Up GVB Calculations For most molecules Lewis dot structures give a reasonable idea of what GVB pairs you should consider setting If you want to automatically assign pairs by Lewis dot structure for input files generated and submitted outside the GUI see Section 8 5 6 on page 165 You do not have to assign all possible GVB pairs You can set GVB pairs in any order If you are studying a dissociating bond you should assign all reasonable GVB pairs for that bond For some purposes such as for dipole moment calculations you may find that assigning only pairs for bonds between two different atoms is sufficient Bonds to hydrogen atoms can also be ignored for some cases You should not assign GVB lone pairs if you are using a minimal basis set since the basis set does not have enough degrees of freedom to handle the lone pair When assigning lone pairs you should only put one GVB lone p
293. from the Solvent option menu and Jaguar performs a solvation calculation setting the appropriate dielectric constant and probe radius The dielectric constant 67 and probe radius 68 values set by Jaguar for various solvents are shown in Table 3 3 Table 3 3 Parameters for various solvents Solvent Dielectric Constant Probe Radius 1 2 dichloroethane 10 65 2 51 benzene 2 284 2 60 carbon tetrachloride 2 238 2 67 chlorobenzene 5 708 2 12 chloroform 4 806 2 52 cyclohexane 2 023 2 78 dichloromethane 8 93 2 33 dimethyl sulfoxide DMSO 47 24 2 41 dimethylformamide 36 7 2 49 methanol 33 62 2 00 nitrobenzene 35 74 2 73 tetrahydrofuran 7 6 2 52 water 80 37 1 40 To use a solvent that is not on this option menu you can define it by choosing Other and changing the entries for Dielectric constant Molecular weight and Density The latter two values are used to calculate the probe radius in angstroms see reference 68 If you compute the solvation free energy of a minimum energy or transition state structure optimized in solution your calculation should compare the energy of the optimized solvated structure to the energy of the optimized gas phase structure Therefore by default geometry 70 Keyword epsout in the gen section 71 Keyword radprb in the gen section Jaguar 7 0 User Manual Chapter 3 Options optimizations in solution are performed only after an optimized gas phase structure is computed However if
294. g 2 Use default convergence criteria shown in Table 8 21 3 Perform quicker coarser calculation by multiplying convergence criteria shown in Table 8 21 by 5 4 Solution phase criteria a factor of 3 times the criteria shown in Jaguar 7 0 User Manual Table 8 21 Chapter 8 The Jaguar Input File Table 8 17 General geometry optimization keywords Continued Keyword Value Description nogdiis 0 Use GDIIS method Geometry optimization by Direct Inversion in the Iterative Subspace 138 to get new geometry 1 Don t use GDIIS method ilagr lt 0 Zero out gradients along frozen coordinates 0 or 1 Project out gradient components in constrained coordinates gt l Apply constraints using Lagrange multipliers nooptr 0 Optimize all bond lengths not specifically constrained in zmat section 1 Constrain freeze all bond lengths for optimization noopta 0 Optimize all bond angles not specifically constrained in zmat section 1 Constrain freeze all bond angles for optimization nooptt 0 Optimize all torsional angles not specifically constrained in zmat sec tion 1 Constrain freeze all torsional angles for optimization ip472 0 Do not save intermediate structures in the mae output file 2 Save intermediate structures in the mae output file Table 8 18 Keywords for transition state optimizations Keyword Value Description iqst 0 Perform standard non QST transition state search 1 Use quadratic synchronous transit QST
295. g istate 1 n Perform calculation on state number n n is the index of the state in the output from hfig for degenerate states in transition metal systems If you want to perform an open shell singlet calculation using UDFT or UHF set ioss 1 This option replaces the alpha and beta HOMO with a mixture of the HOMO and LUMO as follows Q HOMO PHomo PLUMO ie 9 HOMO nouo ruwo 2 The orbitals are taken from a closed shell starting guess The LUMO remains the same This option also sets isymm 0 and iuhf 1 Do not use this keyword for transition metals for which you should use the 2spin column in an atomic section to set up an antiferromagnetic guess Note This starting guess does not correspond to the open shell singlet state but is a mixture of singlet closed shell and triplet open shell states The final wave function in a UHF calculation will not necessarily correspond to what would be obtained in an ROHF calculation and might be a mixture of a singlet and a triplet state You should check the value of S in the output to determine the extent of spin contamination In UDFT calculations exchange is handled differently and all that can be concluded is that the final density represents the lowest state This is more correctly described as a spin polarized method rather than an open shell singlet method for UDFT it yields the correct dissociation behavior for a sigma bond In the transition metal initial guess secti
296. g set for the devel opment of new pK correction parameters Select molecules for which the experimental pK values are accurately known Aqueous pK values near 14 and beyond or near 0 and beyond are not generally accurate because of the difficulty in measuring the concentration of acid or base in the presence of high concentrations of hydronium or hydroxide the leveling effect All of the experimental pK values must be in the same solvent at the same temperature plus or minus a few degrees pK values in mixed solvents are not a good choice This is because the continuum solvation model used by Jaguar requires the specification of a sin gle solvent dielectric constant and probe radius and it is not known how these parameters should be specified for a mixed solvent system especially when the degree of preferential solvation of the solute is unknown Try to obtain experimental pK values that cover as wide a pK range as possible for the given functional group This ensures that the fitting parameters are broadly applicable to molecules containing that functional group The more molecules you use in the training set the more clearly you can see how well the calculated pK correlates with the experimental pK and the better idea you will have of the RMS error Do not select training set molecules that contain symmetrically equivalent functional groups An additional correction term is required in this case to account for the increased
297. gas phase free energy difference between the protonated and deprotonated states can be computed via the usual relations A AH TAS Eg Esme 5 2RT TAS B g Evaluation of this expression requires the following quantum chemical calculations 1 Geometry optimization of the protonated and deprotonated species Quantum chemical methods generally carry out a conjugate gradient optimization and hence cannot search for multiple minima We assume here that there is only a single well defined conforma tional minimum and that a good initial guess obtained for example from molecular mechanics or semiempirical quantum chemistry is available Density functional theory particularly the hybrid methods that include Hartree Fock exchange have been shown to provide good quality geometries we utilize B3LYP 6 31G geometry optimization Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module 2 Accurate single point energies at each optimized geometry must be evaluated These sin gle point calculations are carried out at a significantly higher level of theory than the geometry optimization but since only one energy is required the overall cost of this step is less than that for geometry optimization In recent publications and in our own exten sive unpublished work the B3LYP method with large basis sets has been shown to yield excellent gas phase energetics for deprotonation reactions with errors typically in the 1 3 kcal mol range
298. ge are described 8 5 1 Units Keywords The keywords iunit eunit and espunit set units for geometry energy and electrostatic poten tial units The iunit keyword whose default value is 1 describes what units the geometry is assumed to have as indicated in Table 8 2 It also sets the length units for plot grids and for the location of point charges The eunit keyword sets the energy units for thermochemical proper ties and for harmonic potentials used for harmonic constraints The espunit keyword sets the units for output of electrostatic potentials Jaguar 7 0 User Manual 163 Chapter 8 The Jaguar Input File 164 Table 8 2 Options for the keyword iunit Keyword Value Description iunit 0 Geometry units are bohr and radians 1 Geometry units are angstroms and degrees 2 Geometry units are bohr and degrees 3 Geometry units are angstroms and radians eunit 1 Energy units are kcal mol 2 Energy units are kJ mol espunit 1 Electrostatic potential in units of kcal mol electron Useful for comparing molecules 2 Electrostatic potential in units of kT electron at 298 15 K Useful for comparing molecules 3 Electrostatic potential in atomic units 4 Electrostatic potential in units of kcal mol 5 Electrostatic potential in kT mol at 298 15 K 8 5 2 Covalent Bonding Keyword The real valued keyword covfac determines which atoms are considered to be bonded Two atoms are bonded if they are closer to each other than
299. gence criterion which is described in Section 3 9 on page 48 If the solvation energy has converged the output from the sole program includes a line summarizing the solvation energy iterations and result The output from ch and post appears below the sole output If the solvation energy has converged the ch output reflects the system s final atomic charges If the solvation energy has not converged these charges and the Poisson Boltzmann solver s files generated by the post program are passed to the solver again and the solvation iterations continue as previously described until solvation energy convergence is reached 5 3 5 2 Output from an SM6 Calculation When an SM6 solvation calculation is performed in Jaguar the gas phase wave function is first calculated followed by the solution phase wave function Once the solution phase calculation has completed the various components of the solvation free energy are printed out Atomic L wdin populations atomic redistributed L wdin populations if diffuse basis functions are used Mayer bond orders and CM4 partial atomic charges in the gas phase and solution phase are also computed as part of a normal SM6 calculation Below the output from an SM6 calculation of methylamine in water B97 1 6 31G level of theory is given The input file that was used to generate this output is given here amp gen basis 6 31g dftname b97 1 isolv 5 nops 1 econv 1 0D 8 amp amp zmat N 0 760740 0
300. grid point and each line should list in order the x y and z Cartesian coordinates in angstroms and the weight for that grid point Grid weights are only used in charge fitting so if you don t want to use them use 0 as a placeholder For information about how to use this grid in a Jaguar calculation see Section 8 5 25 on page 210 Comments in the input file are ignored by Jaguar 8 1 2 Sections Describing the Molecule and Calculation The rest of the input file is composed of named sections The sections may appear in any order Character case upper or lower is ignored therefore either case or a combination of the two may be used Equals signs commas blank spaces and tabs are all considered spacing characters however if you plan to use the GUI we suggest that you use equals signs between a keyword and its value and avoid using them anywhere else Blank lines or multiple spacing characters in a row are equivalent to a single spacing character and thus may be used to improve readability The gen section contains a list of the general keywords which control the calculation Defaults are provided for all unspecified keywords The other sections contain lists such as atomic coordinates The sections are listed in Table 8 1 Each section has a distinct format the formats are described in detail in the rest of this chapter Keywords in the gen section can have integer real or character string values Generally valid
301. group as a function of substituents Consider for example carboxylic acids The charge on the oxygens in the CO moiety varies by as much as 0 45 eu when electron withdrawing substitu ents such as in oxalic acid are replaced by electron donating substituents such as in propi onic acid This change in charge alters the hydrogen bonding first shell correction term as well as the solvation free energy computed by the SCRF calculation Since changes in the raw pK are well correlated with these charge shifts linearly scaling the correction term to the raw pK is capable of capturing this effect While corrections to the solvation model are the dominant terms in our empirical corrections there are also intrinsic errors in the gas phase DFT calculations which are implicitly incorpo rated into the correction scheme The assumption is that these errors are systematic for a given functional group This means that the DFT calculations are required only to reproduce the rela tive energetic changes produced by modification of substituents a less demanding task than absolute pK prediction As the accuracy goal 0 5 pK units is beyond the capabilities of the raw DFT calculations empirical corrections are necessary 13 2 Predicting pK Values in Complex Systems The algorithm described in Section 13 1 on page 304 can be straightforwardly applied in the simplest cases which are characterized as follows 1 There is only one relevant ionizable group
302. guar assumes a default formal charge of 0 and multiplicity of 1 for each fragment Note however that any charge or spin multiplicity settings in the atomic section must be compatible with any settings for overall charge and spin specified by the Jaguar 7 0 User Manual 133 Chapter 6 Using Jaguar 134 molchg and multip keywords in the gen section For more information about the atomic section see Section 8 8 on page 219 After saving the input file with the atomic section you can run it in Jaguar in the usual manner You do not need to set iguess because Jaguar will choose the most appropriate guess for the system under study If you have an antiferromagnetic system the standard transition metal initial guesses do not work For an antiferromagnetic system containing two metal atoms that are not bonded you can use a 2spin column in the atomic section to set up the initial guess When the metals are within bonding distance or when there are more than two metals you should assign the metal atoms to separate fragments using the frag column of the atomic section Finally add formal and 2spin values in the atomic section Transition metal systems can have multiple states based on different occupations of the d orbitals If this is the case the initial guess routine prints the possible states and by default continues with the first state However this state might not be the lowest state You should run calculations on all the pos
303. guar run NICE SAVE jobname causes executables to be run with a lower CPU scheduling priority see man page on nice and leaves all temporary files generated during the job in the temporary directory To submit a series of independent jobs you can replace jobname with a list of input file names If you do not specify a host or specify a single host the jobs run sequentially If you specify multiple hosts with the HOST option the jobs are distributed over the hosts specified When a host finishes running a job it starts the next job until there are no more jobs to be run The list of hosts must be separated by spaces and enclosed in quotes For hosts that have more than one processor you can append the number of processors to use to the host name separated by a colon as in the following example jaguar run HOST beta 2 ch4 nh3 You can also use jaguar batch to run multiple jobs If you want to provide Maestro files as input you must use jaguar batch you cannot use jaguar run See Section 10 2 on page 272 for more information 10 1 4 Killing a Jaguar Job The jaguar kill command lets you kill any Jaguar job you are running on any host When you use the jaguar kill command the temporary directory for your job still exists and contains all files generated during the job and no output files are copied back to your output directory To kill one of your Jaguar jobs enter the command jaguar kill jobname This command checks all hosts
304. guar run command can be found in Section 10 1 on page 263 This section describes the submission of jobs from Maestro Regardless of what kind of job you run or where the input is obtained from you can submit the Jaguar job by clicking the Start button in the relevant panel The Start dialog box Figure 2 6 is displayed in which you can enter information on how and where to launch a job This dialog box has two sections the Output section and the Job section For more detailed information on this dialog box see Section 4 2 of the Job Control Guide 2 9 1 Output Handling In the Output section you can choose how the results are incorporated into Maestro at the end of the job using the Incorporate option menu The four options are described in Section 4 8 of the Job Control Guide The choice that you make from this menu is persistent the next time you run a Jaguar job the incorporation mode that you last used is the default mode The incorporation mode is stored as a preference by Maestro so the choice persists across Maestro sessions NE Jaguar jaguar Start Output Incorporate Append new entries as a new group Joh Name benzene Host localhost 1 CPUs 1 Scratch directory scr Mute trageser Start Cancel Figure 2 6 The Start dialog box Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro The results of this job will not be incorpo
305. have converged By default calculations use the DIIS or GVB DIIS convergence scheme which generates an estimate of the Fock matrix that is a linear combination of current and previous Fock matrices determined to minimize the norm of the error vector The keyword maxdiis sets the maximum number of Fock matrices default 10 that are used for this scheme during any iteration The keyword stdiis gives an error criterion DIIS is started when the largest value of the DIIS error vector is less than the value of stdiis hartrees which is 100 0 by default In general after GVB DIIS starts any density matrix averaging requested by the keywords iteravg and istavg explained in Table 8 28 is turned off The keyword vshift sets the amount the virtual orbital energies are increased before diagonal ization in atomic units This keyword can be used to reduce mixing of the real and virtual orbitals which sometimes helps convergence By default vshift is zero except for DFT calcu lations when the default is 0 2 for hybrid methods or 0 3 for non hybrid methods Non default values should probably be on the order of 0 1 0 5 The iacscf keyword may be employed if other attempts to converge the SCF fail This can be useful especially for transition metal containing systems or clusters Start with iacscf 1 and if that does not work then try iacscf 4 iacscf 2 was developed especially for hemes and Jaguar 7 0 User Manual 193 Chapter 8 Th
306. he output format are not discussed in this section 5 3 1 DFT If you use density functional theory for the SCF calculation the output above the SCF table lists the functional or combination of functionals used The energy information for DFT calcu lations includes the breakdown of the two electron energy into Coulomb and exchange corre lation terms For DFT calculations virtual orbitals are obtained by diagonalizing Hy bi f 2J V c where f is the occupation of each orbital 1 for a closed shell For closed shell calculations this definition yields the standard orbitals and eigenvalues The scf output from post SCH DFT energy evaluations GVB DFT calculations for instance first lists the standard output for the HF GVB or DFT SCF calculation then lists the energy breakdown and total energy from the post SCF DFT analysis Since the post SCF DFT treat ment does not change the wave function no orbital output is reported from this step The output from the program pre for non default options contains the detailed description of customized functional combinations for SCF or post SCF DFT calculations 5 3 2 LMP2 If you perform a local MP2 calculation the output from the programs pre and hfig is some what different from that of a Hartree Fock calculation since the use of symmetry is turned off automatically for LMP2 calculations The output from the program scf includes the Coulomb and exchange contributions to the two electron terms
307. hemselves Ref 76 also includes scale factors suitable for use when low frequency vibrations are of particular interest for zero point vibrational energies and for prediction of enthalpy and entropy Other scale factors may be available in the literature 3 11 4 Animation of Frequencies Maestro can display vibrational animations based on Jaguar frequency data This data is written in a file with a vib extension when you perform a frequency calculation For calcula tions that use a Project Table entry as the source of input the vibrational data is incorporated when the job finishes and a Vib column is added to the Project Table The Vib column has a button labeled V for each entry that has vibrational data much like the Surf column has for surface data Clicking the button opens the Vibration panel in which you can select the frequency to be animated and control the amplitude and speed of the animation You can switch modes and change entries during the animation 94 Keyword isqm 1 in the gen section 95 Keyword isqm O in the gen section 96 Keyword scalfr in the gen section Jaguar 7 0 User Manual Chapter 3 Options Table 3 4 Recommended frequency scale factors for various combinations of SCF method and basis set taken from Ref 76 SCF Method Basis Set Scale Factor HF 3 21G 0 9085 HF 6 31G 0 8953 HF 6 31 G 0 8970 HF 6 31G 0 8992 HF 6 311G 0 9051 MP2 6 31G 0 9434 MP2 6 31G 0 9370 MP2 6 311G 0 9496
308. hen you would use the following command jaguar batch counterpoise filename keyword igeopt 1 keyword dftname x3lyp 10 2 4 2 hydrogen bond py The script hydrogen bond py can be used to calculate the total binding energy of a hydrogen bonded complex of two molecules See Section 2 13 on page 28 for details on the computational protocol You can use this script from Maestro or from the command line To run the calculation from Maestro 1 Choose Run Batch File from the Jaguar submenu of the Applications menu The Jaguar Batch panel opens 2 Click the Browse button The Select Batch Script dialog box opens 3 Click Jaguar Scripts The Jaguar batch scripts that come with the Jaguar distribution are displayed in the panel 4 Select hydrogen bond py from the list of scripts and click OK 5 In the Jaguar Batch panel choose the appropriate source from the Source of structures option menu 6 Click Start When the job finishes the optimized structure of the complex is incorporated into the project with the binding energy in kcal mol as a property From the command line use the following command SSCHRODINGER jaguar batch hydrogen bond options filenames Jaguar 7 0 User Manual Chapter 10 Running Jobs Table 10 7 Options for the hydrogen bond py script Option Description noopt Do not perform any optimizations Useful if the input geometries are already accurate noopt complex Do not optimize the geomet
309. here the values of j EL and m determine the exchange and correlation functionals and i specifies particular coefficients for the functionals The functionals themselves are determined as described in Table 8 10 through Table 8 13 Table 8 9 Functional name strings for construction of the dftname keyword Name String S xa b pw vwn5 pl p86 pw91 lyp idft Value 1 9 11 41 100 200 300 1300 4400 2000 Functional Description Slater local exchange XQ local exchange Becke 1988 nonlocal exchange Slater local exchange Perdew Wang 1991 GGA II nonlocal exchange Slater local exchange Vosko Wilk Nusair local correlation Vosko Wilk Nusair 5 local correlation Perdew Zunger 1981 local correlation Perdew Zunger 1981 local correlation Perdew 1986 nonlocal gradient correction Perdew Wang GGA II 1991 local and nonlocal correlation Lee Yang Parr local and nonlocal correlation For instance if idft 1301 the DFT calculation uses the Slater local exchange functional and the Perdew Zunger local correlation functional with Perdew s 1986 non local correlation func tional A typical local density approximation LDA calculation could use idft 101 while idft 2011 sets the popular NLDA choice called BLYP If you specify the Lee Yang Parr func Jaguar 7 0 User Manual 171 Chapter 8 The Jaguar Input File 172 tional which contains local and non local terms you may not specify a local correlation func tio
310. hird party products For details of third party software copyrights terms and conditions see the Legal Notices for Third Party Software at SSCHRODINGER docs html third party legal html Revision A August 2007 Contents Document Conventions aus accu orae Sate ea ee ea xiii Kaprun 1 1 1 About This Manual een scene accuse Back Aeon heeds 1 1 2 Running Schrodinger Software sse 2 1 3 Citing Jaguar in Publications A 2 Chapter 2 Running Jaguar From Maestro 3 2 1 Sample Calculation sss nennen 3 2 2 The Jaguar EE 6 2 3 The Edit J b Dialog BOX opus RePEc Er ee Ee E sere FD M Raa EES 8 2 4 Molecular Structure Input 9 2 4 1 Cartesian Format for Geometry Input esee 10 2 4 2 Variables in Cartesian Inplt E 10 2 4 3 Constraining Cartesian Coordinates eee 11 2 4 4 Z Matrix Format for Geometry Input seeeseeeeeeeeeeneeee 11 2 4 5 Variables and Dummy Atoms in Z Matrix Input 18 2 4 6 Constraining Z Matrix Bond Lengths or Angles ssssesseseersereereereereernsrnernerenne 14 2 4 7 Counterpoise Calculations oo ceci aient teneis cess socks ee esL SI A Sd abu Meneses 14 2 4 8 Specifying Coordinates for Hessian Hefinement 16 2 5 Reading GIGS uscite a Fia ra bcr bau rede Ur DA eee 17 2 6 Setting Charge and Multiplicity AAA 18 2 7 Cleaning up Molecular Geometries
311. ibed below In this fashion all of the errors asso ciated with the various components of the method are subsumed into a small number of param eters characteristic of the functional group in question 13 1 2 Empirical Corrections The results of the above calculation can be assembled to yield a raw pK value Because of the intrinsic errors involved in each step it is necessary to apply an empirical correction scheme to the raw data to yield good agreement with experiment The validity of this scheme can be assessed only by comparison with experimental data For the most important functional groups we have examined a large and diverse set of molecules including those containing polyfunctional groups and conformational flexibility to evaluate the robustness of the method ology For the molecules considered below it appears to be quite satisfactory For example for protonation of nitrogens in heterocycles an average prediction accuracy of 0 19 is obtained over 16 molecules whose pK values range from 0 65 to 9 17 Our empirical corrections take the simple linear form pK apK raw b a That is we assume that the correction terms obey a linear free energy relationship The b term is similar to our previously employed surface tension corrections for solvation of neutral species The linear term takes into account the significant variation in charge on the ionizable Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module
312. ibed in Chapter 4 which also contains more details about the methods used for optimizations Table 8 17 contains general optimization keywords that apply to all kinds of optimizations Most default values for the integer keywords are indicated in bold italics and only the values listed in the table are allowed In cases where the default is different for optimizations to minimum energy structures than it is for transition state optimizations both defaults are in bold italics and the cases for which each is a default are explained in the keyword description Table 8 18 lists keywords specific to transition state optimizations Table 8 19 lists keywords that are used to specify the initial Hessian control Hessian updating and modify the Hessian when using it to update the geometry Table 8 17 General geometry optimization keywords Keyword Value Description igeopt 0 Do not optimize molecular geometry 1 Optimize minimum energy structure 1 Calculate forces but do not perform geometry optimization 2 Optimize transition state geometry Jaguar 7 0 User Manual 177 Chapter 8 The Jaguar Input File 178 Table 8 17 General geometry optimization keywords Continued Keyword Value Description nogas 0 For optimizations in solution perform gas phase geometry optimization first to get accurate solvation energy 1 For optimizations in solution skip gas phase geometry optimization and compute solvation energies using
313. ic populations 3 Perform Pipek Mezey localization on core orbitals for LMP2 calculation maximizing Mulliken basis function populations loclmp2v 1 Perform Boys localization on valence orbitals for LMP2 calculation 2 Perform Pipek Mezey localization on valence orbitals for LMP2 calcula tion maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on valence orbitals for LMP2 calcula Jaguar 7 0 User Manual tion maximizing Mulliken basis function populations Chapter 8 The Jaguar Input File 8 5 8 DFT Keywords To use density functional theory DFT you should set the dftname keyword You can also use the idft keyword which was the only option in versions of Jaguar prior to 5 0 If you want to evaluate the non self consistent energy of the final post SCF wave function using a partic ular set of functionals you can use the jdft keyword Most DFT options described here are also available from the GUI as described in Section 3 3 on page 35 For information on setting the keywords associated with grids for DFT calculations see Section 8 5 25 on page 210 The dftname keyword can be given as a standard functional name as listed in Table 8 8 or it can be constructed from a set of functional name strings for exchange and correlation func tionals which are listed in Table 8 9 The corresponding values of idft are listed along with the functional name strings For example dftname bp86 specifies the BP86 functional an
314. ical gradient freq Calculates vibrational frequencies and related properties ira irb Calculate dipole derivative terms needed for calculation of IR intensities geopt Performs geometry optimization pbf Solves Poisson Boltzmann equations for solvation calculation solv Performs solvation calculation with Poisson Boltzmann solver sm6 Performs solvation calculation with SM6 sole Checks solvation energy convergence dsolv Computes solvation related gradient terms for solvated geometry optimizations post Processes files output etc at end of run timex Checks CPU time for entire run machid Utility program returns machine information not used in Jaguar calculations The simplest form available for the path section is a list of the programs to be run as in the following example amp path pre hfig grid rwr amp It is not actually necessary to list pre in paths since the pre program will always be run Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File If you want to run additional programs after a standard Jaguar calculation you can use the word path to indicate the default path as below amp path path executable list amp More complicated paths involve looping over programs until the last Jaguar program in the loop indicates that convergence is reached The first program in the section of the path to be looped over is preceded by a loop label and the last is followed by a goto label where each of these labels is
315. ided later in the file and dictate the level of analytic corrections the grid and the non default values of the gen section cutoff keywords cut1 for example The cutoff sets are described in more detail below The columns reflect a scheme in which calculations are broken down into preliminary and final sets of iterations The iterations from the beginning of the first SCF calculation in a run are considered to be part of the prelim inary set while the iterations from the end of the first SCF calculation or from any subsequent set of SCF iterations are considered to be part of the final set For instance for a solvation calculation the SCF iterations for the analysis of the converged gas phase wave function are preliminary iterations followed by final iterations while the SCF iterations for all subsequent SCF calculations those including the solvent effects are final iterations Jaguar determines how many iterations are preliminary and how many are final for the initial SCF calculation The number in the first column in each of the five accuracy level lines dictates the cutoff set used for the first iteration in the preliminary sequence if the number is a 1 the first cutoff set listed in the file is used if it is a 5 the fifth is used and so on The number in the second column provides the cutoff set used for updates during the preliminary sequence of iterations The third and fourth columns describe the cutoff sets used for the first and u
316. ify variables for the second and or third geometries in the zvar2 and zvar3 sections If no zmat2 or zmat3 sections exist these variables are used in combination with the zmat section to define the second and third geometries The equation that defines a variable can also specify a range of values for coordinate scans You can assign a list of values to the variable in the format at number list or you can assign the initial value specified by number or rom number and two values from the following list in the order given in the list The final value of the coordinate specified by to number The step size specified by by number The number of steps specified by in integer Here integer means an appropriate integer and number means an appropriate real number See Section 4 4 2 on page 82 for information and examples 8 4 The coord and connect Sections For some geometry or transition state optimizations you might want to specify that the opti mizer use particular internal coordinates For example if you study a bond forming reaction you can require Jaguar to use the bond in question as an internal coordinate even when the bond distance is very long You also might want to generate your own list of internal coordi nates for cases that involve multiple separate unbonded fragments It is often useful to specify internal coordinates for pairs of atoms that are on separate sections of a large floppy molecule but are close to being
317. ifying its x y z coordinates in the same units used for the geometry angstroms by default but bohrs if the iunit keyword in the gen section is set to 0 or 2 see Section 8 5 1 on page 163 for more information The sample pointch section below puts one point charge of charge 1 at location 0 0 0 2 and another of charge 1 at location 0 0 0 4 amp pointch 1 0 0 0 0 2 1 0 0 0 0 4 amp Note that point charges should not contribute to the value of the net molecular charge molchg given in the gen section Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File If you include a non empty pointch section in the input file for a job the output from the program pre includes a table of fixed charge information describing the point charges This table appears in the output file immediately after the molecular geometry output 8 12 The efields Section If you would like to calculate wave functions or molecular properties in the presence of an electric field you may use the efields section to describe this field The x y and z components of the electric field should be specified in atomic units on the same line The requested prop erties will then be calculated for the molecule in the presence of this field The scf output will also include nuclear electric field and electron electric field terms The convention used in Jaguar for electric fields is to add a term of E r to the no field Fock matrix where E is
318. iis 103 solvation 48 51 energy Output nne ertet 105 keywords for 186 187 output from calculations 102 109 probe radius 520 187 Solvent cholCe uh ttes 50 van der Waals radii 102 222 254 262 solvation free energy eT 48 DMG wets dies 51 Solvation tab sinisisi eirese 49 solvent parameters csse 50 SPARTAN archive files 124 207 spin density surface teers 63 215 spin multiplicity KEY WOT 164 setting in Maestro 18 spin populations Mulliken 54 SQM frequency scaling method 60 standard functionals dftname values for 169 standard output key Words acce cei caido seres 204 205 Maestro options eese 121 124 standard state conversion for SM6 solvation 51 Start dialog box etes tieni 22 structure input see geometry input structure optimizing see geometry optimization structures selecting for IRC calculation 86 selecting for transition state optimization 76 submitting jobs see running jobs Superblocks ecce eos tenete 196 Surface Table panel sss 65 Index surfaces displaying in Maestro 64 generating data Tor 63 214 Symmetrize Workspace dialog box 20 symmetrizing geometry input 19 20 288 symmetry effect on structure sissien nense 288
319. ile You can create or edit Jaguar input files by hand making keyword settings corresponding to all of the relevant options described above see Chapter 8 for details If you want you can make some of the desired settings in the GUI use the Jaguar Write dialog box to save a Jaguar input file and edit it by hand later to set other keywords You can generate additional information for the gau file by setting the output keyword ip160 in the gen section of the input file to 3 4 or 5 Setting this keyword to 3 lets you provide an initial guess within the gau file as described for GVB calculations above even if you are doing a non GVB calculation Setting it to 5 allows you to explicitly provide the basis set itself rather than just the basis set name within the gau file This option is useful for speci fying basis sets which are included in Jaguar but not in GAUSSIAN Setting ip160 to 4 allows you to include both the initial guess and the basis set in the gau file Writing Orbitals for GAUSSIAN You can write orbitals from Jaguar in the format used by GAUSSIAN for its guess cards option by choosing to print the appropriate orbitals from the Output tab which is described in Section 5 6 on page 125 You must choose the f19 15 or f8 5 format from the Format option menu Jaguar 7 0 User Manual Chapter 7 Theory This chapter contains a description of some of the theory behind the methods used in Jaguar Section 7 1 describes
320. ilk L Nusair M Can J Phys 1980 58 1200 The VWN correlation functional is described in the paragraph below equation 4 4 on p 1207 while the VWNS functional is described in the caption of Table 5 and on p 1209 Perdew J P In Electronic Structure Theory of Solids Ziesche P Eschrig H Eds Akademie Verlag Berlin 1991 Perdew J P Chevary J A Vosko S H Jackson K A Pederson M R Singh D J Fiolhais C Phys Rev B 1992 46 6671 Becke A D Phys Rev A 1988 36 3098 Lee C Yang W Parr R G Phys Rev B 1988 37 785 implemented as described in Miehlich B Savin A Stoll H Preuss H Chem Phys Lett 1989 157 200 Perdew J P Zunger A Phys Rev B 1981 23 5048 Perdew J P Phys Rev B 1986 33 8822 and Perdew J P Phys Rev B Erratum 1986 34 7406 Jaguar 7 0 User Manual 325 References 326 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 6l 62 63 64 65 Becke A D J Chem Phys 1996 104 1040 Becke A D J Chem Phys 1997 107 8554 Becke A D J Chem Phys 1998 109 2092 Schmider H L Becke A J Chem Phys 1998 109 8188 Schmider H L Becke A J Chem Phys 1998 108 9624 Hamprecht F A Cohen A J Tozer D J Handy N C J Chem Phys 1998 109 6264 Boese A D Handy N C J Chem Phys 2001 114 5497 Perdew J P
321. ill not be set correctly and this error message results Jaguar 7 0 User Manual 299 Chapter 12 Parallel Jaguar 300 If HOME has a value on the compute nodes different from that on the launch node then the secure server daemon serv p4 will not allow MPI processes to be launched on the slave node This is because the daemon expects to find on the compute nodes a file called S HOME server apps that contains the path to the current executable This file is written by the script MPI install bin mpirun ch p4 but this script only runs on the launch host Thus if HOME is different on the launch and compute hosts then serv p4 will not be able to authenticate the user s permission to launch the executable under mpirun If this problem occurs then the error message in the 10g file for the job is simply p4 error Child process exited while making connection to remote process on hostname If HOME cannot be defined consistently the workaround is to manually add the full path to each of Jaguar s parallelized executables to each user s server apps file on the com pute nodes The list of executables is as follows pjexec setup pjexec cleanup pjexec ckerrs allnodeexec mpi spread ppre ponee phfig pgrid prwr pscf plmp2 ppost pder2ndb pcphfa 12 1 3 IBM Installation For IBM you need to install the Parallel Operating Environment POE package which includes the MPI libraries Jaguar requires a version of P
322. ils on jaguar batch commands including command line options Jaguar 7 0 User Manual 27 Chapter 2 Running Jaguar From Maestro 28 2 13 Binding Energies of Hydrogen Bonded Complexes To calculate an accurate binding energy for an intermolecular hydrogen bonded complex you can use the Jaguar batch script hydrogen_bond py see Section 10 2 4 2 on page 280 for instructions This script automates a multi step protocol in which the binding energy is calcu lated using two correlation consistent basis sets cc pVTZ f and cc pVQZ g and LMP2 theory including corrections for basis set superposition error The final correction to the binding energy uses two parameters from a fit of the energies to reference energies that were obtained from CCSD T calculations extrapolated to the basis set limit The binding energies are accurate to within 0 5 kcal mol when compared to the extrapolated CCSD T energies The protocol is based on that described in Ref 28 except that all geometry optimizations are carried out using X3LYP 6 31G instead of LMP2 cc pVTZ f The X3LYP density func tional gives very good geometries for hydrogen bonded complexes and is much faster than LMP2 The energy calculations however are still carried out using LMP2 with the cc pVTZ f and cc pVQZ g basis sets An option is provided to use the DFT energies rather than the LMP2 energies In a test for a series of ten hydrogen bonded complexes the RMS error using
323. in the molecule 2 There is a single relevant conformation of the molecule and this conformation is valid for both the protonated and deprotonated form An example of this situation is acetic acid However it is also possible to use the module in more complex situations In the following sections we explain how this is accomplished 13 2 1 Conformational Flexibility First consider the case in which assumption 1 above holds but the protonated and deproto nated states can each exist in multiple conformations which might be energetically competi tive There are several possible ways in which the conformational problem can be addressed In the current release only method 1 below has been automated It is still possible to carry out the strategies outlined in method 2 however at present you must run multiple jobs and manu ally assemble the data into a final result 1 Perform calculations on one protonated and one deprotonated conformation which are assumed to dominate the phase space due to being lowest in energy in their class This is a reasonable assumption for many problems Note that the lowest energy conformation can be different for the protonated state and the deprotonated state In many cases there Jaguar 7 0 User Manual 307 Chapter 13 The pK Prediction Module 308 are obvious electrostatic reasons why a conformational change upon protonation or deprotonation would occur The program is set up to accept a
324. in this fashion cannot lead to high levels of accuracy because there are large error bars on the experimental data typically 5 10 kcal mole An error of 5 kcal mol in the solvation free energy that was not systematic would lead to huge errors in pK calculations This is because in determining the pK there is a cancel lation of two very large terms the gas phase deprotonation energy which favors the proto nated state and the solvation free energy which favors the deprotonated state Errors in either term therefore can be a small percentage of the total energy but lead to very large errors in the resulting calculated pk To overcome this problem the parameters for ions are fitted directly to experimental pK data If the gas phase quantum chemistry and neutral solvation are reliably computed then the solva tion free energy of the ionic species becomes the remaining unknown quantity Since pK measurements are carried out to quite high precision in contrast to direct measurements of ionic solvation fitting to this data does not lead to the large uncertainties that would be associ ated with the ionic solvation data Additionally there is an exceptionally large database of known pK values for a wide range of chemical functional groups Jaguar 7 0 User Manual 305 Chapter 13 The pK Prediction Module 306 In general the dielectric radii of ions particularly negative ions are expected to be smaller than that for the corres
325. in van der Waals contact Otherwise small changes in a torsional coordinate far away from these atoms can then lead to steep changes in Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File the energy Adding explicit coordinates for these non bonded contacts makes it possible for the optimization algorithm to control their approach more effectively To control the internal coordinates used in an optimization you should first make sure that Jaguar is going to generate internal coordinates for the job Optimization jobs generate and use redundant internal coordinates unless you have set the keyword intopt in the gen section of your input file See Section 8 5 10 on page 177 for more details To specify that particular bonds or angles should be included in the internal coordinates gener ated and used for an optimization use a coord section Each line of a coord section should contain a list of atoms used to specify a bond bond angle or torsional angle coordinate to be included among the internal coordinates generated by Jaguar 8 4 1 Constrained Coordinates If you want to hold a coordinate fixed at its initial value throughout the job add the entry to the end of the line after one or more spaces As an example the coord section amp coord Cl C2 cl C2 C3 f cl C2 C3 C4 amp requests that the set of internal coordinates include the C1 C2 bond the C1 C2 C3 bond angle which is to be held frozen throughout the
326. ine F or ultrafine U See Section 8 5 25 on page 210 and Section 9 4 on page 248 if you want more information on grids and grid types The total energy for the molecule in Hartrees appears in the next column followed by the energy change from the previous iteration to the current one The RMS density change column provides the root mean square of the change in density matrix elements from the previous iteration to the current one In the last column the maximum DIIS errors listed provide a measure of convergence by listing the maximum element of the DIIS error vector For HF and DFT closed shell calcula tions the DIIS error vector is given by FDS SDF in atomic orbital space where F D and S are the Fock density and overlap matrices respectively For open shell and GVB cases the definition of the error vector is given in reference 11 After the energy information for each SCF iteration a summary of the components of the final converged energy is given Each of these energies is labeled with a letter for example A for the nuclear repulsion and information to the right of some of the energies describes the rela tions between the components in terms of these letters A line below the table summarizes the calculation type and energy as well as the number of SCF iterations If the input system s spin multiplicity is not singlet the summary of the SCF output also includes a breakdown of the two electron contribution to the
327. ine grid used by default 1 Calculate electron density on grid and write chdens file in a format that can be converted to a file Anthony Nicholls program Grasp can read using ps2grasp f available from Schr dinger run with geldens 3 and denspcz 0 3 or smaller for best results denspc 0 75 Spacing in bohrs of rectangular grid for electron density calculation mulken 0 Do not calculate Mulliken populations 1 Calculate Mulliken populations by atom 2 Calculate Mulliken populations by basis function and by atom 3 Calculate Mulliken bond populations nmr 0 Do not calculate NMR shielding constants 1 Calculate NMR shielding constants The finite field methods corresponding to ipolar gt 0 differ in the data they use for numerical differentiation The 3 point method uses the results from seven SCF calculations one with no field one with a field of E whose input is described below in the x direction one with a field Jaguar 7 0 User Manual 189 Chapter 8 The Jaguar Input File 190 of E in the x direction and four others with fields of E and E in the y and z directions The 5 point method uses the same data as the 3 point method as well as data from SCF calcula tions using fields of aE and aE in the x y and z directions where a is some constant Simi larly the 7 point method uses the same data as the 3 point method plus data obtained using fields of aE aE bE and bE in the x y and z direct
328. ing described in Section 4 3 3 on page 77 because any eigenvector selected for following should be accurate enough to be a reasonable representation of the final transition vector To refine an initial Hessian select Hessian refinement in the Transition State tab then enter the number of low frequency Hessian eigenvectors to be used in the refinement in the Low frequency modes text box By default no eigenvectors are used that is no refinement is performed unless the input specifies particular coordinates for refinement Hessians can be refined using any number of the lowest frequency Hessian eigenvectors Refinements involve SCF and gradient calculations for displacements along these modes which allow more accu rate information about the most important modes to be included in the Hessian You can also specify particular coordinates for Hessian refinement If you put an asterisk after a coordinate value Jaguar computes the gradient of the energy both at the original geom etry and at a geometry for which the asterisk marked coordinate has been changed slightly and uses the results to refine the initial Hessian to be used for the optimization To request refine ment of a coordinate whose value is set using a variable add an asterisk to the end of the vari able setting in the line at the end of the geometry input that defines the variables For instance either of the following two input geometries would use both O H bonds and the H O H
329. ing example is interpreted in the same way as the gen section example given above This is a comment amp gen iguess 0 molchg 1 amp This is also a comment 8 2 The zmat zmat2 and zmat3 Sections The molecular geometry must be described in the zmat section Details on entering a geometry through the GUI can be found in Section 2 3 on page 8 and Section 2 4 on page 9 The units for the geometry are set by the iunit keyword of the gen section by default these units are angstroms and degrees If the geometry is in Cartesian coordinates each line must contain four items an atom name and the x y z coordinates Each item should have at most 80 characters The atomic label should begin with the one or two letter elemental symbol in either uppercase or lowercase characters Additional alphanumeric characters may be added as long as the atomic symbol remains clear for instance HE5 would be interpreted as helium atom 5 not hydrogen atom E5 Up to eight characters can be given in an atomic label A sample Cartesian zmat section for a water molecule is amp zmat O 0 000000 0 000000 0 113502 H1 0 000000 0 753108 0 454006 H2 0 000000 0 753108 0 454006 amp A zmat section in Z matrix format should not include lines defining variables which are set in the zvar section described in Section 8 3 on page 159 and should not contain any comment lines but otherwise should have the same format as described in Section 2 4 4 Section 2 4
330. installation instructions 1 Install the MPT package if it is not already installed You can check to see if MPT is already installed with the following command IRIX showprods grep MPI Altix rpm q sgi mpt 2 Install Array Services if it is not already installed You can check to see if Array Services is installed with the following command IRIX showprods grep arraysvcs Altix rpm q sgi arraysvcs 3 Start the array services daemon with the following command etc init d array start This daemon can be configured to start automatically at system startup with the command chkconfig array on l Please see the notice regarding third party programs and third party Web sites on the copyright page at the front of this manual Jaguar 7 0 User Manual Chapter 12 Parallel Jaguar You should also check that the Scientific Computing Software Library SCSL for distributed shared memory SDSM 1ibsdsm so is installed On Altix machines running SLES 10 this library is not installed by default You can obtain the library by installing the SCSL package which is available from http www sgi com products evaluation 12 1 2 Linux x86 and Linux ia64 non Altix Installations For Jaguar to run in parallel on a multiprocessor machine the Linux kernel must be compiled to support symmetric multiprocessing SMP For Linux Jaguar is dynamically linked to two MPI compatibility libraries of our own design The source code for
331. int group that approximately describes the structure and use that group to symmetrize the molecule instead of the default The tolerance is also used when the molecule is symmetrized After translation and rotation the coordinates of the atoms are adjusted to reflect the symmetry group accurately The maximum displacement permitted is the tolerance specified A large tolerance yields the highest symmetry but may cause the coordinates to be changed significantly A small tolerance may yield a lower symmetry but results in smaller coordinate changes The main Jaguar programs use a small tolerance 1 0 x 10 bohr which should result in molecular energy changes of 1 microHartree or less You can turn the use of symmetry off in the Molecule tab For methods such as GVB LMP2 GVB LMP2 and for some properties such as IR intensities or hyperpolarizabilities symmetry is not yet implemented and is disabled automatically for the job If you are comparing calculations from geometries that differ only slightly you must use caution when symmetrizing coordinates For example a small symmetry breaking change can be removed if its magnitude is smaller than the tolerance you have set which establishes what changes are acceptable In this case you should inspect the symmetrized coordinates in the Edit Job dialog box to insure that symmetrizing had the desired effect and did not discard any important information about the molecular geometry 5 Keyword is
332. ion Since for a Hessian H H j Hi only the elements with j i are read in and the program symmetrizes the matrix itself later Since the Hessian has dimensions of 3Nx3N where N is the number of atoms including dummy atoms it may be large so files listing all elements in each row by order of rows could be unwieldy and difficult for the user to read Therefore the Hessian is assumed to be presented in blocks composed of five columns each with the last block possibly having fewer than five columns if 3N is not a multiple of five The format used for the hess section is the same as that used in GAUSSIAN files or BIOGRAF hes files All Hessian elements for dummy atoms should be set to 0 as they are in Jaguar output Each set of elements from a block of five columns should be preceded by a line containing one or more arbitrary integer labels for instance column labels could be convenient for keeping track of the elements when looking at the hess section All of the elements within a five column block for which j the column indicator is less than or equal to i the row indicator are then read in one row at a time Each row of five or fewer matrix elements starts with an arbi trary integer label this integer is not used in the program but can be used to label the row for example When the relevant matrix elements from that entire five column block have been read in the next block is read in the same way until all of the matrix ele
333. ion 4 4 3 on page 83 for more information Harmonic constraints can be set on the Cartesian position of an atom or on any bond length angle or dihedral angle by adding hc or HC after the coordinate The Cartesian position is specified by a single atom label as in the following example amp coord Cl hc 10 0 amp Two atom labels specify a bond three labels a bond angle and four labels a dihedral angle as usual The value of a force constant for the harmonic potential must follow hc or HC in units specified by the gen section keywords iunit and eunit The force constant can be followed by the radius a of a region in which the constraining potential is zero and this radius can be followed by a target value for the coordinate if it is an internal coordinate A target value cannot be specified for a Cartesian harmonic constraint The following example specifies a harmonic constraint on a bond length with a force constant of 10 0 kcal mol A a radius of 0 5 and a target bond length of 1 5 amp coord C1 C2 hc 10 0 0 5 1 5 amp Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File 8 4 2 Specifying Bonds for Internal Coordinates with a connect Section You can use a connect section to specify the bonds used by Jaguar in its generation of internal coordinates Each line of a connect section should list two atoms by either their atom labels such as H2 for a hydrogen or their atom numbers such as 3 for the third ato
334. ions where a and b are some constants By default the magnitude of the electric field E is 0 024 au If you want to use a different value set the efield keyword to the desired value All polarizability methods are run with symmetry off that is the keyword isymm is set to 0 automatically if ipolar 0 Similarly for any polarizability calculation the keyword econv which gives the energy convergence criterion is set by default to 1 0x10 although if the calculation first satisfies the criterion dictated by the keyword dconv the energy convergence criterion is ignored When charge fitting is constrained to reproduce multipole moments that is when inedip gt 0 the keyword cfiterr determines whether the multipole moment constraint is too restrictive to produce adequate charges if the error in the total resultant charges is more than cfiterr the charge fitting is rerun with a lower multipole moment constraint The keyword wispc is used to set the spacing of the rectangular grid for electrostatic potential fitting when the grid keyword gcharge 2 Similarly the keyword denspc is used to set the spacing of the electron density rectangular grid when Idens 1 and the grid keyword geldens 3 The efield keyword allows you to specify an electric field for finite field polarizability and hyperpolarizability calcula tions The default value shown in Table 8 25 applies when ipolar gt 1 For ipolar 1 3 point polarizability only calculations th
335. ions produce some population and charge properties by default These are described in Section 3 10 7 on page 57 The Properties tab has a table of available properties and an area below the table where controls for a property are displayed when you select the table row for the property To include the calculation of a property in a job select the check box in the Calculate column Vibrational frequencies and related properties and surfaces are discussed in later sections This section focuses on the remaining properties 3 10 1 Charges from Electrostatic Potential Fitting Jaguar can fit the molecular electrostatic potential ESP to a set of point charges 70 71 These monopoles can be located either at the atomic centers or at the atomic centers and the bond midpoints depending on the selection from the Fit ESP to option menu The atomic charges are written to the output Maestro mae structure file and are available in Maestro as the partial charge These charges can then be used in other applications such as MacroModel or QikProp 75 Keyword icfit 1 in the gen section 76 Keyword icfit 2 in the gen section Jaguar 7 0 User Manual Chapter 3 Options Jaguar jaguar la Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Properties select to edit options L Property Vibrational frequencies Surfaces MO density potential
336. is set used for atoms not described by ECPs S indicates the STO 3G basis set D indicates the D95V basis set and P indicates the 6 31G set developed by Pople and coworkers Note that in addition for some atoms the LACVD and LACVP basis sets use the same basis functions as the LAV3D and LAV3P basis sets respectively The Los Alamos effective core potentials which were developed by Hay and Wadt include one electron mass velocity and Darwin relativistic corrections for elements beyond Kr The Cundari Stevens ECP basis set 116 named CSDZ has been provided to cover the lanthanides This basis set uses a relativistic effective core potential for the inner core electrons and treats the outer core and valence electrons with a 4s 4p 2d 2f basis set Jaguar 7 0 User Manual 33 Chapter 3 Options 34 Table 3 2 Basis sets contained in Jaguar that include effective core potentials Basis Set Atoms in ECP Other Atoms Options Refs LAVIS Na La Hf Bi H Ne STO 3G H Ne 109 110 LAV2D Na La Hf Bi H Li Ne D95V H Li Ne 109 110 LAV2P Na La Hf Bi H Ne 6 31G H Ne 109 110 H Ne LAV3D Na La Hf Bi H Li Ne D95V H Li Ne 109 110 LAV3P Na La Hf Bi H Ne 6 31G x H Ne 109 110 H Ne LACVD K Cu Rb Ag H Li Ne D95V Na Ar H Li Ne 111 Cs La Hf Au Zn Kr Cd Xe Hg Bi LAV3D LACVP K Cu Rb Ag H Ar 6 31G Zn Kr c H Ar 111 Cs La Hf Au Cd Xe Hg Bi LAV
337. is a local MP2 calcu lation and you want to see the energy from each LMP2 pair use the gen section keyword setting ip170 2 as described in Section 8 5 21 on page 204 5 3 3 GVB If a GVB calculation is performed from a Hartree Fock initial guess the pre program output lists a table of GVB pair information below the list of non default options Since the use of symmetry is turned off automatically for GVB calculations the output from the programs pre and hfig is somewhat different than for a Hartree Fock calculation Also the program gvbig runs after hfig if the GVB initial guess is being generated from the HF initial guess The output from the scf program is more extensive than for a default HF calculation First the number of GVB pairs and the number of GVB orbitals are added to the list of electron and orbital information preceding the table of SCF iteration information Secondly the summary of the SCF output is followed by a breakdown of the two electron contribution to the energy into Coulomb and exchange parts For each of these parts the contribution from each GVB Hamil tonian is listed After this information the intra pair exchange energies and their sum are listed Finally a table of GVB pair information is given Here is an example of this GVB infor mation in the SCF output for a water molecule with two GVB sigma pairs Total Coulomb Exchange Total two electron terms 37 90378136033 46 96140169504 9 05762033471 Hamiltonian 1
338. is expected to decrease and the binding energy is expected to increase in magnitude The binding energy extrapolated to the basis set limit is printed last For especially weakly bound systems it occa sionally happens that the energy obtained with the cc pVTZ f basis set is slightly lower than that obtained with the larger cc pVQZ g basis set In this situation the usual two point basis set extrapolation formula cannot be used so the energy is instead corrected using a simple linear correction of the LMP2 cc pVQZ g energies to the CCSD T reference energies The Jaguar 7 0 User Manual 281 Chapter 10 Running Jobs output file clearly indicates when this has happened The binding energy will still be quite accurate to within 0 5 kcal mol when compared to the CCSD T energy 1 This is likely due to the fact that the BSSE corrections are calculated only for the Hartree Fock part of the wave function rather than for the full LMP2 wave function which would be more expensive The error in this approximation amounts to a few tenths of a kcal mol 282 Jaguar 7 0 User Manual Chapter 11 Troubleshooting Naturally we hope that you will never need to use this chapter However if you have problems using Jaguar you may find useful advice here If you don t feel free to contact us as described on page 322 For problems with settings you might find the information you need in the online help You can obtain help from any pa
339. issions on it from the root account Use the command 1s 1 to get information on ownership of your temporary directory or the directory above it If you need to be able to create a subdirectory within a directory owned by root or another account that does not belong to you and for which you do not have write permission contact your system administrator for help 11 1 5 Problems Running Jaguar Calculations on Other Nodes In order to launch jobs on other nodes and for these nodes to copy files back to the host from which they were submitted the nodes must be able to run rsh remote shell and rcp remote copy commands on each other If you get a Permission denied error when trying to start a job the rsh command is not being allowed This problem may occur even if the job submis sion host the submission host and the host where the calculation is to be performed the execution host are the same The best method to test whether this problem is occurring is to issue individual rsh commands at a submission host command line prompt such as rsh execution host who where you substitute the name of the host where you want to perform the calculation for execu tion host If both the local and execution hosts are on the same local network ask your system manager about allowing rsh commands between the two which could be done in several ways depending on your system One way is to list hosts which are allowed to connect using rsh to a g
340. itals printed depends on whether five or six d functions are specified for the basis set as described in Section 3 2 on page 30 Each iteration in AO space Print orbitals after each SCF iteration in atomic orbital space By default no orbitals are printed in the output file so None is selected by default in the Orbitals option menu If you select Occupied orbitals all occupied orbitals including GVB 15 Keyword ip165 3 in the gen section 16 Keyword ip175 2 in the gen section 17 Keyword ip102 in the gen section 18 Keyword ip105 in the gen section 19 Keyword ip104 in the gen section 20 Keyword ip107 in the gen section 21 Keyword ip101 in the gen section 22 Keyword ip103 in the gen section Jaguar 7 0 User Manual 125 Chapter 5 Output 126 natural orbitals are printed If the All orbitals option is selected all occupied orbitals and ten virtual orbitals are printed To change the default of ten virtual orbitals see the keyword ipvirt in Section 8 5 24 on page 207 The virtual orbitals are obtained by diagonalizing Hoyt 3 f 2J EI where fis the fractional occupation of each orbital 1 for a closed shell The format for printing the selected orbitals can be chosen from the Format option menu The choices available are Large elements as f5 2 labels in list All elements as f10 5 labels in table All elements as f19 15 in list All elements as f8 5 in list All elem
341. ithin a few seconds Forinformation about a panel or the tab that is displayed in a panel click the Help button in the panel The help topic is displayed in your browser For other information in the online help open the default help topic by choosing Help from the Help menu on the main menu bar or by pressing CTRL H This topic is dis played in your browser You can navigate to topics in the navigation bar If you do not find the information you need in the Maestro help system check the following sources Maestro User Manual for detailed information on using Maestro Maestro Command Reference Manual for information on Maestro commands Maestro Overview for an overview of the main features of Maestro Maestro Tutorial for a tutorial introduction to basic Maestro features Jaguar Quick Start Guide for a tutorial introduction to Jaguar Jaguar Frequently Asked Questions pages at https www schrodinger com Jaguar FAQ html The manuals are also available in PDF format from the Schr dinger Support Center Informa tion on additions and corrections to the manuals is available from this web page Jaguar 7 0 User Manual 321 Getting Help 322 If you have questions that are not answered from any of the above sources contact Schr dinger using the information below E mail help schrodinger com USPS Schr dinger 101 SW Main Street Suite 1300 Portland OR 97204 Phone 503 299 1150 Fax 503 299 453
342. iven host in its etc hosts equiv file It may be necessary to include the name of the submission host in its own etc hosts equiv file if the calculation is to be done on the submission host See your system manager or your UNIX documentation concerning trusted hosts NIS domains or networking for more information If you get an error which refers to problems writing or changing to a temp directory for the job you should make sure that you have permission to write to the directory specified in the Scratch directory option menu in the Start dialog box and that you have permission to create that directory if it does not already exist If you are unable to allow rsh commands as described above e g your local and execution hosts are not local to each other you must include the local machine in a rhosts file in your home directory on the execution host and vice versa If you have the same user name on both nodes a line in the rhosts file only needs to contain the entire host name For more informa tion see the rhosts man page on your machine One further complication can result if you have distinct user names on the local and execution hosts In this case you may get an error like one of the following Jaguar 7 0 User Manual 287 Chapter 11 Troubleshooting 288 Login incorrect remshd Login incorrect rshd xxxx xxxx The remote user login is not correct This problem generally occurs only when the local and execution ho
343. junoo x ngeur 7Z 19AO0 oouopoooud ap uomnoes ormunje Y ur sgurjos jeu pue suioje osrodaojunoo Ajtoods o3 uorjoes 20001 201 VSN ULI NOX eAnrsues SLI JOU TE A UO pue ouou 200 0 sonpeA aq SUIOJ PASH 107 soS1euo Ieo onu 10 suoroung Sursei vop sjurod pus pnpour oj JayjoymM Ajroeds 0 nok MOJE rg AQEL ut uMous spIOM 9 JOYIO INL Uorjoes MWO OY esueqo Udy pue Apojo duroo uonoes ssan 201 ojo op ULIO NOA A oAneuloj y Or TO OUXTUI ur uorjes ssan y ur poyroeds ssons pentur y sjoudaojursiur ure18odd IY ASTMIOYIO Je W uoroos 20016 OY o3ueqo jou eur no amp uor no eo p o oy Surj1e3so1 qof puooss 10 o y 1ndur sty aen noA Jr mq qof y WoT ur TO oux ru po eo Y 3183591 e y ndur Mou oj amp 1ouo8 ULI NOA suloj JUDIOJJIP IOF sjos srseq JUI JJIP saytoods yey uoroos oruroje ue surejuoo UT TOUXTUI e y ndur ssoym qof e uni nod Jt oougjsur IOJ gol JOY 34D1s24 4210 NOK fi sjuauuudissp Jas sisnq Kun AR HDH jou pynoys nok ndui au ui SWUOJD 42110 IYI AOL pasn Jas sispnq 211 unu SUWOW 2401 40 IUO AOL sj2s sispq Juasaffip amp fi22ds o1 uouoos onuojp HD asn NOK JT T E UON ur pequosop os e SI S oqui amp s osou JO Surueoui au OULU siseq ou 193 A ojerpoului JO gy x Surpuodde Aq poppe oq ued suonoung osngrp pue uonezie oq pasn oq ueo s19jj9 eseo1oddn 10 oseo1oA0 T T E uoroos ur Sat ou Jo uuin oo js1ij 201 uio3j uosouo eq prnoys JOS SISeq au equosop 0 peprAoJd Surns ou s
344. k CPHF terms for LMP2 dipole moments 40 55 for LMP2 ESP fitted charges 40 53 covalent radii usse 222 cpolar program we 234 rh 204 Culot Fletcher method for trust radius adjustment keyword ss 181 cutoff file default description and format 252 specifying in input file sseeeeeeeeeeee 155 cutoff method 45 68 194 Index CUO S ceci 194 195 196 252 253 shown in output eere 95 128 D daf file defa lt niit etes 237 description and format 243 248 neighbor ranges 243 244 specifying in input file 155 dealiasing functions 31 243 choices for calculation 244 contracted 244 245 246 keyword for list in output 204 key WOFdS coe rete ttn rne 210 211 long range eee 243 245 246 neighbor ranges for 123 243 245 ordering of sets eee tes 245 output of number used 204 short range eee 243 245 246 uncontracted sseooseneeesseieeeeee0eeeeene 244 245 default atomtog Die 242 delocalization of LMP2 pairs 168 218 density difference matrix keyword for output of 208 RMS of elements in output
345. k Create Properties For any entry that has these properties set you can set the charge and spin multiplicity for the calculation by selecting Use charge and multiplicity from Project Table 2 7 Cleaning up Molecular Geometries The molecular geometry sometimes needs improvement before you perform calculations For example it might not have the desired molecular symmetry or it might be far from the minimum or transition state Maestro has options to clean up the geometry for calculations in both of these cases The options are available from the Build panel which you can open by clicking the Open Close Build panel toolbar button in the main window F 2 7 4 Quick Geometry Optimization You can clean up the geometry by clicking the Clean up geometry button in the Build panel K 2 Keyword molchg in the gen section 3 Keyword multip in the gen section Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro Maestro first performs a quick charge equilibration Qeq calculation to obtain partial charges for all atoms in the system and then uses those charges in an energy minimization based on Goddard and Rappe s Universal Force Field UFF Because UFF includes parameters for all elements in the periodic table it can be used for inorganic complexes as well as organic compounds During the UFF minimization a status box is displayed To stop the minimization click Stop in this status box The convergence criteria fo
346. ke on nonzero values when basis functions corre sponding to different values as described in the next column use primitive Gaussians with the same exponents Positive values indicate that the same exponents are used in the shell listed that number of rows down a value of 1 indicates that the exponents are provided from a shell listed earlier The values in the next column indicate the angular momentum a value of 1 corresponds to an s function 2 indicates a p function 3 a d function and so on The nfsh values are zero based pointers to the basis function list The column labeled z lists the exponents for the primitive Gaussians while the coef column lists the coefficient of their contribution to the linear combination comprising the basis func tion Note that the uncontracted basis functions those with jcont values of 1 have coef values of exactly 1 Finally the product of the coef value and the normalization constant for the primitive Gaussian shell N is listed in the column labeled rcoef Gaussian Functions Shell information S j h GE n e Oo S t 1 n h S atom n id h a coef rcoef O 1 6 0 1 0 5484 6716600 0 0018311 0 8317237 Oo 2 1 240 7 0 825 2349460 0 0139502 1 5308156 Oo 3 zs 1 0 188 0469580 0 0684451 2 4771485 O 4 1 0 7 0 52 9645000 0 2327143 3 2562811 O 5 l 30 3 0 16 8975704 0 4701929 2 7928934 Oo 6 S150 1 0 5 7996353 0 3585209 0 9549377 O 7 3 ge 1 15 5396162 0 1107775 0 6179340
347. l Chapter 9 Other Jaguar Files spectral calculations use 0 as a place holder for each range value Pseudospectral calculations require that grids and dealiasing functions exist for the basis set These are defined in the default grid and default daf files respectively see below The Gaussians in the contraction are listed next with the first number in each of these lines describing the exponent for the Gaussian and the second its coefficient in the contraction The Gaussians should be listed in decreasing size of exponent If both s and p functions are being described the second number on the line corresponds to the coefficient for that Gaussian in the s function s contraction and the third number corresponds to the p function s contraction coef ficient The data for that atom ends with a line containing 4 characters with no spaces or other characters preceding them When all of the atoms for that basis set have been listed ending with the obligatory line the next basis set is listed in the same manner described above The beginning of the default basis file is shown below to illustrate most of these points BASIS STO 3G S TO3G STO 3 H STO3 5D S 0 2 1 1 0 3 42525091400000 0 623913729800000 0 168855404000000 KKKK He S 0 3 2 6 36242139400000 1 15892299900000 0 313649791500000 KKKK Li S 0 3 4 16 1195747500000 2 93620066300000 0 794650487000000 0 154328967294599 0 5353281422
348. l 26 and must be in a format recognized by Babel Maestro does not read any Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro 18 information other than the geometry from these files If you want other information such as a Hessian you can cut and paste it into a Jaguar input file 2 6 Setting Charge and Multiplicity Apart from the geometry the main setting that you might want to make in an otherwise default calculation is to set the molecular charge and the spin multiplicity You can set these quantities in the Molecule tab The default molecular charge is determined by the formal charges on the atoms in the Workspace The default spin multiplicity is 1 singlet if the molecule has an even number of electrons and 2 doublet if it has an odd number of electrons You can change the charge by entering a value in the Molecular charge text box and you can change the spin multiplicity by entering a value in the Spin Multiplicity 294 1 text box The spin multiplicity is always displayed in this text box If the molecular charge and spin multiplicity settings you make do not agree with your molecular input for instance if your molecule has an odd number of electrons and you set the spin multiplicity to 1 Maestro warns you of the inconsis tency and you must choose consistent values to submit a job The charge and spin multiplicity can be stored in the Project Table as properties of the mole cule To do so clic
349. l Correlation Functional k 0 none k 1 Vosko Nusair Wilk VWN k 2 VWN5 k 3 Perdew Zunger 1981 k 4 Perdew Wang GGA II 1991 local correlation only Table 8 13 Values of j in idft where idft ijkim jin idft Non local Correlation Functional j 0 none j l Perdew 1986 nonlocal gradient correction IEN Lee Yang Parr local and nonlocal correlation Jaguar 7 0 User Manual 173 Chapter 8 The Jaguar Input File 174 Table 8 13 Values of j in idft where idft ijklm Continued jin idft Non local Correlation Functional j 3 HCTH407 nonlocal correlation functional j 4 Perdew Wang GGA II 1991 nonlocal correlation only j 6 Becke 1998 B98 nonlocal correlation functional EN Schmider and Becke 1998 SB98 nonlocal correlation functional j 8 B97 1 nonlocal correlation functional j 9 PBE nonlocal correlation functional Table 8 14 Values of i in idft where idft ijkim i in idft Hybrid Method i 0 none i 1 half amp half functional coefficients are all 0 5 i 2 Becke 3 parameter parameters from ref 32 i 3 Becke 1998 B98 i 4 Schmider and Becke 1998 SB98 i 5 Becke 1997 reparametrized B97 1 For Becke 3 parameter hybrids you need to specify a Slater or Xo local exchange functional a non local exchange functional a local correlation functional and a non local correlation functional i e j k l and m must all be non zero if i is 2 Even when you use the Lee Yang Parr functional in a Becke
350. lable for array for example or the log file indicates Killed for the job Your job may have failed because the machine was too heavily loaded in which case rerunning the job when the load is lower could solve the problem Otherwise you might want to try an appropriate setting from Section 8 5 26 on page 212 to avoid a problem for a large job or you and or your system manager might want to investigate increasing the maximum virtual size or the soft limit allowed for memory on your machine Contact us as described on page 322 if you would like any tips for setting memory use for your machine Jaguar 7 0 User Manual 289 290 Jaguar 7 0 User Manual Chapter 12 Parallel Jaguar The parallel implementation of Jaguar is based on MPI Message Passing Interface Jaguar can run on SMP symmetric multi processing shared memory architectures such as worksta tions that contain multiple processors and it can run on distributed memory architectures such as IBM SP clusters or Linux Beowulf clusters Jaguar can also run on clusters in which each node contains multiple processors The development of parallel Jaguar is discussed in refer ences 171 and 172 The following kinds of jobs can be run in parallel HF and DFT single point calculations in gas phase or in solution HF and DFT geometry optimizations in gas phase or in solution HF and DFT second derivative calculations vibrational frequencies Closed shell LMP2 si
351. lained in Chapter 7 GVB calculations include what is sometimes called non dynamical electron correlation To run a GVB calculation you must define atom pairs and orbital types that you want to be treated with the GVB method In the GVB Pairs section of the Theory tab you can select All atom pairs or Heteroatom pairs Heteroatom pairs include all atom pairs except C atoms Jaguar 7 0 User Manual 43 Chapter 3 Options 44 bonded only to C and H atoms If you compute solvation free energies using GVB or LMP2 as described in Section 3 9 on page 48 we recommend using heteroatom pairs for the GVB calculation for the most efficient results since solvation free energy calculations often use radii optimized for calculations with heteroatom pairs set See Section 9 6 on page 254 for more details If you want to select other pairs you can do so by adding a gvb section to the input file If you add a gvb section the Level of theory is set to Other The GVB method in Jaguar does not include the concept of resonance Consequently the GVB pair input for a molecule such as benzene for example should include alternate single and double bonds for its carbon ring If you perform a GVB geometry optimization on a molecule with equal resonating bonds like the carbon bonds in benzene you should force the opti mizer to keep their bond distances the same even if the input lists different bond orders for the bonds To impose this restriction
352. le moments are calculated from the atomic Mulliken populations as well as directly from the wave func tion as noted in Section 3 10 2 on page 54 The output lists the multipole moments from the wave function as described earlier the Mulliken populations as described just above and finally the recalculated moments resulting from the Mulliken charges in the same format used for the earlier moment output 5 3 7 5 NBO Calculations Output for NBO calculations appears under the heading Jaguar NBO 5 0 5 3 8 Frequency IR Intensity and Thermochemistry Output If you calculate vibrational frequencies any SCF calculations during the run use the RMS density change convergence criterion described in Section 3 8 on page 45 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed for several more iterations than single point energy calculations do To compute the Hessian for vibrational frequencies Jaguar calculates the second derivatives either analytically or numerically as the derivatives of the analytical first derivatives depending on the type of calculation see Section 3 11 on page 58 for details Whenever numerical second derivatives are computed after an SCF calculation whether for frequency output for an initial Hessian or for updating during geometry optimization the programs nude onee hfig grid rwr scf der1a rwr and der1b run setting up and performing SCF calculations and ev
353. liasing functions available in the grid and dealiasing grid and daf input files which are described in Section 9 3 on page 243 and Section 9 4 on page 248 and from the grids generated within Jaguar These keywords are used to specify which grid or dealiasing sets correspond to particular descriptions this correspondence is often indicated by keyword values depending on the order of sets in the grid and dealiasing input files For density functional theory calculations the grid keywords gdftmed gdftfine gdftgrad gdftder2 and gdftcphf select various predefined grids for the SCF gdftmed and gdftfine gradient second derivative and CPHF calculations The grids are indexed with negative numbers The default values for these keywords are 10 11 12 8 and 9 They can be assigned other values for example 13 corresponds to an ultrafine grid and 14 to the largest DFT grid that can be defined in Jaguar which has 125 radial shells and uses an angular offset of 30 434 angular points per shell with no pruning To use such a grid throughout a geometry optimization you would set the following keywords gdftmed 14 gdftfine 14 gdftgrad 14 You can also define your own DFT grids using three keywords which specify the number of radial shells the number of angular points per shell the pruning scheme and the distribution of the radial shells The keywords and their settings have the form ndfgrdX1 nr ndfgrdX2 na id
354. license request that you want to run pK calculations 13 4 2 Running pK Calculations from Maestro To set up and submit pK calculations from the Jaguar panel in Maestro choose pKa from the Jaguar submenu of the Applications menu The Jaguar panel opens with a modified Molecule tab displayed In this tab you can choose the pK atom in several ways Select Pick to the right of the Use this atom text box and pick the desired atom in the Workspace structure You should ensure that there is only one entry in the Workspace when you pick the pK atom Jaguar 7 0 User Manual 311 Chapter 13 The pK Prediction Module 312 Jaguar jaguar DIE Use structures from Workspace included entries Molecule SCF Solvent Symmetry Use if present 4 Molecular state v Use charge and multiplicity from Project Table Create Properties Use these values Molecular charge 0 J Spin multiplicity 25 1 E pKa atom Use this atom N1 W Pick wv Use pKa atoms from the Project Table Job pKa Start Read Write Edit Reset Close Help Figure 13 1 The Molecule tab for pK calculations Enter the atom label in the Use this atom text box The atom label is the label used in the input file and corresponds to the atom name in Maestro To display atom names for the Workspace structure choose Atom name from the Label atoms button menu in the main toolbar P
355. llows the pseudospectral method to be used See Table 3 1 on page 32 and Table 3 2 on page 34 to obtain this basis set information Because the available basis sets are not designed for core correlation you should not use the mp2 1 setting Calculations performed with this setting are likely to be misleading and can have large pseudospectral error Local MP2 calculations use the LMP2 method for all atoms unless the Imp2 section described in Section 8 7 on page 218 is used to set local LMP2 pairs or unless the keyword iheter is set to 1 The iheter and mp2 keyword settings are described in Table 8 7 For LMP2 calculations Jaguar needs to obtain localized orbitals By default Jaguar uses the Pipek Mezey method to perform the localization If Pipek Mezey localization does not converge for a particular case you might want to try Boys localization by changing the settings for the keywords loclmp2c and loclmp2yv as indicated in Table 8 7 If you are performing a set of calculations to compare against each other you should use the same localization method for all of the calculations Jaguar 7 0 User Manual 167 Chapter 8 The Jaguar Input File 168 Table 8 7 Keyword settings for local MP2 calculations Keyword Value Description mp2 0 Do not run LMP calculation 1 Correlate core and valence electrons not recommended see text 3 Run LMP calculation for valence electrons only iheter 0 Treat all atoms with LMP2 if
356. local density functionals gradient corrected pure density functionals and hybrid functionals which include a Hartree Fock exchange contribution as well as local and nonlocal functionals Most of the hybrid methods employ either the parameters developed for Becke s three parameter method 32 33 Becke 3 or the parameters developed for Becke s Half amp Half method 31 The option menus also contain some recently developed hybrid and non hybrid functionals The functionals available from the option menus are described below LDA Local Density Functionals Functionals with local exchange only e HES Slater local exchange functional 34 Xalpha Xa local exchange functional 34 Functionals with local exchange and local correlation e SVWNP Slater local exchange functional 34 Vosko Wilk Nusair VWN local correla tion functional 35 e SVWN5 Slater local exchange functional 34 Vosko Wilk Nusair 5 VWN5 local correlation functional 35 Gradient Corrected Functionals e BLYP Exchange Slater local functional 34 Becke 1988 nonlocal gradient correction 37 correlation Lee Yang Parr local and nonlocal functionals 38 e BPW91 5 Exchange Slater local functional 34 Becke 1988 nonlocal gradient correc tion 37 correlation Perdew Wang 1991 GGA II local and nonlocal functionals 36 e BP86 6 Exchange Slater local functional 34 Becke 1988 non local gradient correction 37 correlation Perdew Zunge
357. lows you to list them in the output file in atomic units as well as in the default units debye Bond lengths and angles When this option is turned on the internuclear distances in angstroms are listed for all nearest neighbor atoms in the output from the program pre and the bond angles in degrees are given as well D The atoms are indicated with the atom labels assigned in the geometry input When you optimize a geometry this option is turned on automatically For geometry optimizations bond lengths and angles are also listed with the output from the program geopt echo section constructed and keywords mtest 2 and ip24 2 in the gen section Keyword ip5 2 in the gen section Keyword ip6 2 in the gen section Keyword ip26 2 in the gen section Keyword ip25 2 in the gen section Keyword ip11 2 in the gen section Qu UAE Ser ps Jaguar 7 0 User Manual Chapter 5 Output Connectivity table The connectivity table provided by this option describes roughly how closely the atoms interact Connectivity partially determines whether molecular fragments exist the content of the initial Hessian and many other properties of a calculation The assignment of dealiasing functions for the pseudospectral method also depends upon the connectivities shown in this table which reflect the neighbor ranges defined in the dat file See Section 9 3 on page 243 for more information All of the diagonal entries are 0 indicating th
358. ls press gt 0 Pressure for thermochemical calculations from frequencies in atm default is 1 0 tmpini gt 0 Initial temperature for thermochemical calculations in K default is 298 15 tmpstp gt 0 Temperature step size difference between consecutive temperatures for thermochemical calculations in K default is 10 0 ntemp gt 0 Number of temperatures at which thermochemical properties are com puted default is 1 Jaguar 7 0 User Manual 191 Chapter 8 The Jaguar Input File 192 The thermochemical properties are listed in cal mol K and kcal mol by default Use the output option eunit 2 for output in J mol K and kJ mol When the calculation of vibrational frequencies is requested with ifreq 1 for closed shell Hartree Fock calculations intensities for the IR active vibrational modes are automatically calculated irder is set to 1 automatically For any other level of theory you must explicitly set irder 1 and the derivatives must be calculated numerically by setting nmder 2 The calculation of IR intensities involves the calculation of the dipole moment derivatives If you only want to calculate dipole moment derivatives using the Hartree Fock method but don t want to do the frequency calculation that is normally required to get them you must set up a special path section see Section 8 16 on page 233 with the appropriate sequence of executa bles to run The path section to use is amp path pre onee hfig probe grid rwr scf
359. ls First the total of the terms with no electron contribution is listed term A followed by terms B and C the nuclear nuclear and nuclear solvent energies Jaguar 7 0 User Manual Chapter 5 Output Next the total one electron energy is listed along with its three components the electron nuclear electron solvent and kinetic energies The total two electron energy and the total of the one and two electron energies the electronic energy follow Term N the total of the zero one and two electron terms is then listed with the label Total quantum mech energy This term corresponds to the final energy from the scf energy table for that iteration and includes the entire energies for the molecule solvent interactions The output next includes the gas phase and the solution phase energies for the molecule since these terms are of course necessary for solvation energy calculations The first solution phase energy component is the total solute energy which includes the nuclear nuclear electron nuclear kinetic and two electron terms but no terms involving the solvent directly The second component of the solution phase energy is the total solvent energy which is computed as half of the total of the nuclear solvent and electron solvent terms since some of its effect has already changed the solute energy Third a solute cavity term which computes the solva tion energy of a nonpolar solute of identical size and sh
360. m gas phase energy and geometry optimizations but not property calculations All local MP2 geometry optimizations employ analytic gradients For calculations of LMP2 dipole moments Jaguar computes a coupled perturbed Hartree Fock CPHF wave function which can be computationally expensive However since CPHF methods lead to a better description of the charge density we recommend computing LMP2 dipole moments as well for any calculation for which you need to compute accurate LMP2 electrostatic potential ESP fitted charges For details see Section 3 10 1 on page 52 and Section 3 10 3 on page 55 40 Keyword icis 1 in the gen section 41 Keyword nroot in the gen section 42 Keyword maxciit in the gen section 43 Keyword mp2 3 in the gen section Jaguar 7 0 User Manual Chapter 3 Options Jaguar jaguar DIE Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Level of theory LMP2 Local MP2 LMP2 Core localization method None zi Valence localization method Pipek Mezey 1 Resonance None zd LMP2 Pairs All atom pairs Hetero atom pairs Job LMP2 6 31G Single Point Energy Solvation Start Read Write Edit Reset Close Help Figure 3 3 The Theory tab showing LMP2 controls Jaguar s implementation of the local MP2 method requires basis sets that allow the pseudo spectral me
361. m listed in the zmat section input Here is a sample connect section amp connect CL c2 c2 c3 amp The two atoms on each line of the connect section are then treated as nearest neighbors by the program when it generates redundant internal coordinates for the optimization Consequently the internal coordinates generated by Jaguar include the bond between those two atoms and angles between those two atoms and any other atoms that are nearest neighbors to either of them For the sample connect section above for instance the redundant internal coordinates would include the C1 C2 bond the C2 C3 bond and the C1 C2 C3 angle in addition to whatever internal coordinates would be generated without the connect section 8 5 The gen Section The keywords of the gen section allow control over how the calculation is performed Many of these keywords can be set from the GUI See Chapter 3 and Chapter 5 for details Throughout this section the default values for keywords are indicated in bold italics The keywords for geometry input are described first followed by those relating to correlation methods optimization to a minimum energy structure or transition state calculations in solu tion calculation of various molecular properties basis sets SCF methods and output These subsections correspond to the order of information in Chapter 3 and Chapter 5 Finally keywords relating to grids and dealiasing functions cutoff parameters and memory usa
362. mation from each geometry SCF or gradient calculation be reported in a different row of the results table For instance the command jaguar results title all iterg echange gmax grms dmax drms dftg out here produces a table showing the convergence of a BLYP geometry optimization of water Geopt Energy Gradient Gradient Displace Displace iter change max rms max rms 1 3 22E 02 2 65E 02 5 53E 02 4 88E 02 2 2 04E 03 3 85E 03 3 18E 03 2 79E 02 1 70E 02 3 7 04E 05 4 19E 04 3 82E 04 1 45E 03 1 01E 03 4 1 04E 06 3 05E 05 2 52E 05 6 13E 05 5 13E 05 Jaguar 7 0 User Manual 91 Chapter 5 Output 92 The last section of Table 5 1 lists options for specifying when to report intermediate and final results from jobs The a11 option which lets you track the progress of a geometry or transi tion state optimization is likely to be the most useful of the options The allscf option can be used for intermediate results in complex non optimizations such as solvation jobs 5 1 3 Reporting Results for Each Atom By default each line of output from a jaguar results command lists information that pertains to the entire input structure but you can also request some kinds of information for each individual atom in the structure The options that let you print tables of coordinates forces or charges for individual atoms are listed in the per atom information options section of Table 5
363. ment see Section 9 6 2 on page 257 for more information while the right most digit specifies the number of bonds to elements and hybridization types that do not fit into any of the groups described for the element of the atom being evaluated For example suppose only one hybridization group were described for carbon in the sample Lewis file as follows 6 CARBON Group 1 C C sp3 bonds 1 hybridization Sp3 hybridization 1 atom 6 Then this atom type description line in a Lewis file would accurately match the middle carbon in propylene H C CH CH 6 lt 1 1 127 1 4 2 00 C in H2 C C or H2 C 0 as would the following line which also contains the proper settings for the middle carbon s hybridization and bonding type 6 6 111 12 1 1 2 00 C in H2 C C or H2 C 0 Jaguar 7 0 User Manual 261 Chapter 9 Other Jaguar Files 262 As for the integer describing bonding type the total of the digits in the fourth integer should be the same as the number of bonds three for this example remembering that the double bond counts as one bond that is all bonds should be accounted for unless of course the integer is 1 The fifth and sixth integers describe the ring the atom is in if any If the fifth integer is a posi tive number n it indicates that the atom description corresponds to an atom in a ring of size n For example a benzene carbon is in a ring of size 6 If the fifth number is a negative number n the descri
364. ments for the lower triangle of the matrix have been entered For example in the unlikely event that you wanted to enter this Hessian 11 21 31 41 51 61 71 8l 21 22 32 42 52 62 72 82 31 32 33 43 53 03 73 83 41 42 143 44 54 64 74 84 51 52 53 54 55 65 75 85 61 62 63 64 65 66 76 86 71 72 B 74 75 76 7 87 81 82 383 84 85 86 87 88 you would need to enter the elements from the bottom triangle of the Hessian shown in bold in the following way amp hess j i 11 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File i 21 22 i 31 32 33 i 41 42 43 44 i 51 52 53 54 55 i 61 62 63 64 65 i 71 72 73 74 75 1 81 82 83 84 85 J i 66 i 76 77 i 86 87 88 amp where i and j indicate integer labels not actually used by the program 8 10 The guess Section If an input file has a non empty guess section the keyword iguess in the gen section is set to 1 and an initial guess for the wave function is read from the guess section If the label basgss is given the coefficients given in the guess section are interpreted as coefficients of functions from the basis set specified with this label For instance amp guess basgss 6 31g If no basgss setting is given or if basgss is set to non_standard the basis set for the guess is that specified by the basis keyword setting in the gen section You should ensure that the initial guess given in the guess section is for the this basis set Otherwise a poor or meaningless guess is obt
365. mic acid 0 6 1 4 imide 0 9 1 5 barbituric acid 0 2 0 4 tetrazole 0 6 1 4 pyrazoline 0 6 1 1 ACIDS in DMSO NH acid 1 5 2 8 CH acid 1 6 3 4 BASES primary amine 0 5 0 8 secondary amine 0 5 0 9 tertiary amine 0 4 1 1 aniline 0 2 0 6 amidine 0 3 0 5 hydrazine 0 3 0 6 310 Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module Table 13 1 Functional groups for which pKa parameters are available Continued Maximum RMS Absolute Functional Group Deviation Deviation heterocycle 0 2 0 4 benzodiazepine 0 3 0 3 guanidine 0 5 0 8 pyrrole 0 2 0 3 indole 0 2 0 3 a for protonation at the substituted N b for C 2 protonation c for C 3 protonation 13 4 Running pK Calculations pK calculations consist of a series of calculations on the protonated form and on the deproto nated form of the target molecule followed by an empirical correction The calculations are performed using a Jaguar batch script You need only supply an input file with the acidic or basic atom marked and use the batch script to run the calculation You can set up pK calcula tions in Maestro or prepare the input files in a text editor and submit the jobs from the command line 13 4 1 Activating the pK Module The pK module is installed automatically when you install Jaguar but you need a special license to run pK calculations in addition to the regular Jaguar license When you request a Jaguar license you should explicitly indicate in your
366. miltonians used for the calculation shells and the calculation type Next the energy output from the SCF iterations is shown in table form Some of the text for the column headings should be read down rather than across The number of the iteration is provided first in each row followed by a Y or N indicating whether the Fock matrix was updated or not When the Fock matrix is updated the changes are made using a difference density matrix whose elements reflect the changes in the density matrix elements from the previous iteration to the current one The next entry indicates whether the DIIS convergence scheme was used for that iteration As above Y or N indicate yes or no The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices including the one calculated during that iteration DIIS which is enabled by default usually starts on the second iteration and is not used on the final iteration If the entry in this column reads A it indicates that DIIS was not used for that iteration but the density matrix was averaged The cutoff set for each iteration is indicated under the icut heading Cutoff sets are explained in the cutoff file description in Section 9 5 on page 252 Jaguar 7 0 User Manual 95 Chapter 5 Output 96 The grid column lists the grid used for that iteration which must be one of the grid types coarse signified by a C medium M f
367. molecules that include atoms with negative charges For the basis set that you select a message giving the number of functions and stating whether pseudospectral grids are available and whether ECPs are used is displayed below the controls Table 3 1 lists the available basis sets in Jaguar that do not use effective core potentials The table indicates the atoms these basis sets can describe and shows which sets include the options of polarization and diffuse functions The cc pVDZ and cc pVTZ basis sets include polariza tion functions by definition Keyword isymm 8 in the gen section Keyword isymm 8 and idoabe in the gen section Keyword isymm 0 in the gen section Keyword basis in the gen section PS Ree Jaguar 7 0 User Manual Chapter 3 Options Jaguar jaguar DE Use structures from Selected structure files zi Files f zonel dyall 1 10 phenanthroline mae Browse Molecule Theory scr Properties Solvation Output Symmetry Use if present Molecular state v Use charge and multiplicity from Project Table Create Properties Use these values Molecular charge o Spin multiplicity 25 1 1 Basis set 6 31G Polarization 4 Diffuse None Number of D functions w 5D 6D 120 basis functions Start Read Write Edit Reset Close Help Figure 3 1 The Molecule tab Table 3 1 also indicates the method used for the calcul
368. mple the input O 0 000000 0 000000 0 113502 H1 0 000000 0 753108 0 454006 H2 0 000000 0 753108 0 454006 describes a water molecule Each atomic label must start with the one or two letter element symbol and may be followed by additional characters as long as the atomic label has eight or fewer characters and the atomic symbol remains clear For example HE5 would be interpreted as helium atom 5 not hydrogen atom E5 The atom label is case insensitive The coordinates may be specified in any valid C format but each line of the geometry input should contain no more than 80 characters 2 4 2 Variables in Cartesian Input Coordinates can also be specified as variables whose values are set below the list of atomic coordinates This makes it easier to enter equal values and also makes it possible to keep several atoms within the same plane during a geometry optimization To use variables type the variable name zcoor for instance where you would normally type the corresponding numerical value for each relevant coordinate You can prefix any variable with a or sign When you have entered the full geometry add one or more lines setting the variables For instance the Cartesian input O 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 describes the same water coordinates as the previous Cartesian input example If you performed a geometry optimization using this input str
369. n 1 file c3d2 Chem3D Cartesian 2 file cdct ChemDraw Conn Table file diag DIAGNOTICS file dock Dock Database file wiz Wizard file contmp Conjure Template file Cssr CSD CSSR file dpdb Dock PDB file feat Feature file fhz Fenske Hall ZMatrix file gamin Gamess Input file gcart Gaussian Cartesian file gzmat Gaussian Z matrix file gotmp Gaussian Z matrix tmplt file gr96A GROMOS96 A file gr96N GROMOS96 nm file hin Hyperchem HIN file icon Icon 8 file idatm IDATM file Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 31 Output format keywords and file types for babel file format conversions Continued Format Keyword File Type sdf jagz jage m3d macmol macmod micro mm2in mm2out mm3 mmads mdl miv mopcrt mopint csr pcmod pdb psz psc report smiles spar mol mol2 maccs torlist tinker MDL Isis SDF file Jaguar Z Matrix file Jaguar Cartesian file M3D file Mac Molecule file Macromodel file Micro World file MM2 Input file MM2 Output file MM3 file MMADS file MDL Molfile file Mollnventor file Mopac Cartesian file Mopac Internal file MSI Quanta CSR file PC Model file PDB file PS GVB Z Matrix file PS GVB Cartesian file Report file SMILES file Spartan file Sybyl Mol file Sybyl MoD file MDL Maccs file Torsion List file Tinker XYZ file Jaguar 7 0 User Manual 203 Chapter 8 The Jaguar Input File 204 Table 8 31 Output format keywords and file
370. n Table 8 43 The radius settings can be altered by making vdw settings in the atomic section of an input file as described in Section 8 8 on page 219 You can also print out the values of the electrostatic potential at grid points whose locations you specify see Section 8 5 14 on page 187 3 10 2 Mulliken Population Analysis Mulliken populations 73 can be computed for each atom giving a representation of the mole cule as a set of nuclear centered point charges For open shell cases Mulliken spin popula tions are also computed when Mulliken populations are requested If you choose to calculate both Mulliken populations and multipole moments the multipole moments are computed from the atomic Mulliken populations as well as from the wave function Mulliken populations can be computed for each basis function as well as for each atom or for each bond between neighboring atoms as well as by atom and basis function by choosing the appropriate option in the Method section 78 Keyword gcharge 1 in the gen section 79 Keyword gcharge 2 in the gen section 80 Keyword wispc in the gen section 81 Keyword mulken 1 in the gen section 82 Keyword mulken 2 in the gen section 83 Keyword mulken 3 in the gen section Jaguar 7 0 User Manual Chapter 3 Options 3 10 3 Multipole Moments Jaguar can compute multipole moments through hexadecapole for HE GVB or DFT wave functions and can compute dipole moments
371. n coordinate itself must be constrained The way around this is to define what is called a natural torsional coordinate whose value is an average of all possible torsional coordinate values about a specified bond To do this you only need to specify the bond in a coord section and mark it with nt to designate it as a natural torsional coordinate Jaguar automatically determines all of the torsional angles about this bond averages them and constrains the averaged coordinate to its initial value in an optimization Because a natural torsional coordinate is an averaged value it is not possible to scan this coor dinate To map out the potential about a torsion that is specified by a natural torsional coordi nate you would also specify an additional dihedral angle and scan that angle As an example suppose you want to map out the torsional potential about the C C bond in 1 chloro 1 fluoroethane You would specify the C C bond as the natural torsion and scan a dihe dral angle say the F C C CI angle Your coord and zvar sections would look like this amp coord C1 C2 nt F3 C1 C2 cl4 s amp amp zvar s 0 to 180 by 30 amp 4 4 4 Restarting Scans Scan jobs do not store a record of their progress If you want to restart a scan job that stopped prematurely you must edit the restart file to ensure that the scan starts at the appropriate point 4 4 5 Scan Results The results of scan jobs started from Maestro are incorpor
372. n coordinate list For example in the following input for optimization of a water molecule the H atoms are only allowed to move within the xy plane in which they started 0 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor Jaguar 7 0 User Manual 71 Chapter 4 Optimizations and Scans 72 ycoor 0 753108 zcoor 0 454006 If frozen Cartesian coordinates are included in the input for an optimization Jaguar uses Carte sian coordinates for the optimization rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry You can also freeze the average of a set of all possible dihedral angles about a given bond This average is called a natural torsional coordinate To set up a natural torsional coordinate you specify the bond in a coord section and mark it with nt as in the example below Jaguar automatically determines all of the torsional angles about this bond averages them and constrains the averaged coordinate to its initial value in an optimization amp coord C1 C2 nt amp 4 2 2 Applying Harmonic Constraints Sometimes you don t want to entirely freeze the value of a coordinate but allow it to vary within defined limits You can then optimize the geometry while allowing for small variations of coordinates that you know should remain essentially the same You can achieve this end by applying harmonic constraints Harmonic constrain
373. n pairs natom number of atoms symmetry molecular symmetry nsymm symmetry number charge molecular charge multip spin multiplicity s2 spin lt S 2 gt sz2 spin Sz lt Sz 1 gt method SCF post SCF method Energy related options energy final molecular energy enuc nuclear repulsion energy egas gas phase energy esoln solution phase energy esolv solvation free energy esolute solute energy Jaguar 7 0 User Manual Chapter 5 Output Table 5 1 Options for the jaguar results command Continued Option Meaning esolvent solvent energy ereorg solvent reorganization energy homo HOMO energies lumo LUMO energies gap HOMO LUMO energy gap zpe Zero point energy entropy entropy S at 298 15 K enthalpy enthalpy H at 298 15 K gibbs Gibbs free energy G at 298 15 K cv heat capacity C at 298 15 K int_energy Utot Htot Gtot pka pkb dipole internal energy U at 298 15 K Total internal energy U at 298 15 K including the SCF energy and zero point energy Total enthalpy H4 at 298 15 K including the SCF energy and zero point energy Total Gibbs free energy G at 298 15 K including the SCF energy and zero point energy pK pK total dipole moment Geometry optimization options iterg stepg zvar name grms gmax drms dmax echange geopt iteration number geopt step number z variable value must be followed by zvar name rms gradient m
374. n section 37 Keyword irc 1 in the gen section Jaguar 7 0 User Manual Chapter 5 Output The output from a Jaguar run always includes a Jaguar output file which contains the primary output a log file which contains a job summary that is updated as the job is being run and a Maestro formatted file which contains the geometry and properties in a form that can be read by Maestro and other Schr dinger software If you request other output options in the Output tab of the Jaguar panel various other files can also be generated as output This chapter begins with a description of the jaguar results utility which can be used to obtain summaries of Jaguar results The chapter continues with a description of the Jaguar output file for a standard Hartree Fock calculation followed by a discussion of the changes in the output for various other calculation options and the output options that can be set in the Output tab The final section explains the log file which is the file displayed in the Monitor panel as a job runs Throughout this chapter footnotes indicate the Jaguar input file keywords and sections that correspond to particular GUI settings If you are working from the GUI you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the GUI 5 1 Summarizing Jaguar Results You can obtain summaries of Jaguar results in simple table form by using the following comma
375. n types of files in order to run a job An input file must be created of course but additional files specifying the basis functions data for the initial guesses dealiasing func tions grids and cutoffs used during a run are generally necessary as well Unless other files are specified in the input data Jaguar uses the files default basis default atomig default daf default grid and default cutoff which are in the data directory For many solvation calculations Jaguar also uses the file default 1lewis All of these files are provided in the Schr dinger product distribution If you want to use other data files than those described above you can create a new data direc tory and put files in it whose names and formats match those described above When you run a job you can edit the input file and add BASISFILE ATOMIGFILE DAFFILE GRIDFILE CUTOFFFILE or LEWISFILE lines with the paths and names of the files you want to use See Section 8 1 on page 155 for more details You should avoid naming a cutoff file accurate cutoff quick cutoff or solvent cutoff because the program assumes you are using an outdated file and resets the name to default cutoff This chapter contains descriptions of the basis atomic initial guess dealiasing function grid cutoff and Lewis files Even if you do not plan on creating your own versions of these files you might want to skim this chapter if you are curious about the methods used in Jagua
376. nal i e if j 2 k must be 0 unless you are using the Becke 3 parameter hybrid method as described below If the value of i in idft is 1 or 2 the functionals given by j k L and m are combined using coef ficients determined by the appropriate hybrid method as indicated in Table 8 14 For the half amp half hybrids half of the exact exchange is automatically included with half of the selected exchange functional The coefficient of any local correlation functional or non local exchange or correlation functional is also set to 0 5 You must specify a Slater or Xa local exchange functional for a half amp half hybrid and if you use the Lee Yang Parr functional you may not specify a local correlation functional Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 10 Values of m in idft where idft ijkim m in idft Local Exchange Functional or Exact Exchange m 0 exact exchange Hartree Fock m 1 Slater m 9 Xa Table 8 11 Values of I in idft where idft kim lin idft Non local Exchange Functional 1 0 none IEN Becke 1988 nonlocal term only ER Becke 1998 B98 nonlocal exchange functional l 4 Perdew Wang GGA II 1991 nonlocal exchange only l 6 Schmider and Becke 1998 SB98 nonlocal exchange functional l 7 HCTH407 nonlocal exchange functional l 8 B97 1 nonlocal exchange functional l 9 PBE nonlocal exchange functional Table 8 12 Values of k in idft where idft ijklm kin idft Loca
377. nal and duplicated entries as input The other tabs available for pK calculations are the SCF tab in which you can make settings to control the SCF convergence and the Solvent tab in which you can choose the solvent If you chose a pK atom for a CH acid or an NH acid you must choose DMSO as the solvent otherwise the solvent should be water These are the only solvent choices for pK calculations Once you have selected the target molecule or molecules set the pK atom selected the solvent and adjusted settings for the SCF convergence click Start and make job settings in the Start dialog box then click Start again to submit the job See Section 2 9 on page 22 for infor mation on job settings You can distribute a job for multiple molecules across multiple proces sors When the pK jobs are incorporated on completion the pK value is added as a property to the Project Table 13 4 3 Jaguar Input Files for pK Calculations You can prepare a Jaguar input file for a pK calculation using a text editor The input file must contain a molecular geometry and a labeled pK atom The pK atom is either an acidic hydrogen in acids or conjugate acids or a non hydrogen atom to be protonated in bases or conjugate bases The pK atom can be marked by setting the gen section keyword ipkat to either the atom s name or to the atom s order number in the zmat section Here are two equivalent input file examples for formic acid Jaguar 7 0 User
378. nates for Hessian refinement should not be added in this dialog box they are removed when you close the dialog box 2 4 Molecular Structure Input After you start Maestro the first task for setting up any Jaguar calculation is to enter a molec ular structure geometry You can create a structure using Maestro s Build panel you can use the Jaguar panel to read in a file as described in Section 2 5 on page 17 or you can enter and edit the geometry yourself in Cartesian x y z coordinates or in Z matrix format using the Edit Job dialog box This section describes the input formats for Cartesian and Z matrix geom etries The geometry input is used to set constraints of bond lengths or angles for geometry optimization and to specify atoms for a counterpoise calculation These aspects of geometry input are explained in this section as well The geometries that you enter are displayed in the Workspace in which you can rotate and translate the structure change the geometry display in various representations and perform many other tasks For information on Maestro see the Maestro User Manual 1 The geometry input is in the zmat and zvar sections of the input file Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro 10 2 4 1 Cartesian Format for Geometry Input The Cartesian geometry input format can consist of a simple list of atom labels and the atomic coordinates in angstroms in Cartesian x y z form For exa
379. nce criteria 69 182 coordinate system sseeseeeeeee 70 eigenvector following 78 179 180 frozen bond lengths or angles 70 74 in solution sese 51 178 initial Hessian 16 69 70 78 80 159 180 KEY Wof Scenen 177 182 level shifting of Hessian 181 limiting step size for 181 182 maximum iterations sese 69 178 refinement of initial Hessian 16 78 80 159 160 180 search method 75 trust radius 181 181 182 updating of Hessian ees 180 trial wave function see initial guess troubleshooting eee 283 289 trust radius for optimizations 181 181 186 U units electrostatic potential 164 for geometry sss 73 158 162 key WOT 5 uineis mbi rien 164 output Options s sssssssesesiesseseeeserssresreeen 122 unrestricted wavefunctions keyword for cete 194 setting for utilities jagconvert makejbasis Inplch ces V van der Waals adi 221 for ESP fitting ctii 54 for solvation calculations 186 input file sections for 219 221 listed in output eee 103 setting from Lewis file data 298 van der Waals surfaee 54 variables in geometry input 10 11 13 14 71 74 159 160 Jaguar 7 0 User Manual 345 Index
380. nd jaguar results option list output file list Jaguar searches the output files you specify for the information you request through the command options The order of the options determines the order in which the corresponding data is printed The options are listed in Table 5 1 grouped into classes You can also obtain a list of supported options by entering the command jaguar results help The tables produced by jaguar results can describe results from one job or several jobs The results can be restricted to final results from each job listed the default or can include inter mediate results SCF energies for each geometry in an optimization for instance By default each line lists information that pertains to the entire input structure but you can also request some kinds of information for each individual atom in the structure Each of these types of Jaguar 7 0 User Manual 87 Chapter 5 Output results tables are described below Data values for each output file are printed with results for each job on a separate line Table 5 1 Options for the jaguar results command Option Meaning Job and molecular information options jobname job name longjobname job name with wider output stoich stoichiometry weight molecular weight basis basis set nbasis number of basis functions nelectron number of electrons npair number of electron pairs nsigma number of sigma electron pairs npi number of pi electro
381. nd of the run or just prior to any problems encountered Jaguar 7 0 User Manual 137 Chapter 6 Using Jaguar 138 6 6 Conformational Searches Jaguar and MacroModel can be combined into a very powerful tool for finding the preferred conformations of molecules MacroModel is used to perform the search through conforma tional space to identify the lowest energy conformations Jaguar is then used to refine the geometries of the lowest energy conformers Redundant conformers can then be removed from the data set When performing conformational searching of ligands we recommend either the mixed torsional sampling low mode algorithm or the ligand torsional search method The former algorithm combines a random search of torsional space with an extensive following of low mode eigenvectors on the potential energy surface to ensure good sampling of low energy torsions The Ligand Torsion Search method does not use any random sampling and therefore avoids the problem of generating the same conformers repeatedly This method analyzes the molecular structure to identify torsions which might have associated minima and it generates all potential minimum energy structures systematically However the quality of the conformers it produces is not high and more work may be needed to correct the structures See Chapter 9 and Chapter 10 of the MacroModel User Manual for more information about these conformational search methods By default each conf
382. ne during an optimization by setting their coordinates along one axis to the same variable To use variables to set coordinate values from the Edit Job dialog box first type the variable name zcoor for instance where you would normally type the corresponding numerical value for each relevant coordinate You can put a or sign immediately before any variable and you may use several variables if you want When you have entered the full geometry add one or more lines setting the variables For instance in a geometry optimization using the following Cartesian input 0 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 Jaguar 7 0 User Manual 73 Chapter 4 Optimizations and Scans 74 the H atoms remain in the same xy plane and the same xz plane the molecular symmetry is preserved Optimizations are run without symmetry when Cartesian input with variables is used 4 2 4 Applying Dynamic Constraints Dynamic constraints also called soft or harmonic constraints are implemented by means of Lagrange multipliers A dynamic constraint on a geometric coordinate is met gradually during the course of an optimization One advantage of using a dynamic constraint on a vari able is that you can choose a value that is different from its current value For example if you have a complex structure whose conformation you want to change and you know that changing a pa
383. need to change the atomig file correspondingly and vice versa For other basis sets the wave functions used to construct the initial guess are obtained by projecting the appropriate atomic wave function in default atomig onto the basis set actu ally being used for the molecular calculation The 6 31G wave function is used whenever possible when a 6 31G atomic wave function is not listed for a particular atom the MSV wave function is used for that atom For atoms beyond Xe in calculations using the LAV 1S basis set the LAV2P atomic results are used Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files As in the default basis file the basis sets listed in the default atomig file are listed in turn and for each basis the information for each atom is listed Each basis set section begins with a blank line which is followed by one or more lines reading BASIS followed by one space and ending with the name or names separated by a space and or comma of all basis sets for which the atomic calculations listed immediately after that line apply The basis set names are listed in Table 3 1 on page 32 and Table 3 2 on page 34 Next the information for each atom follows The first line lists the atomic symbol for the atom followed by information which is simply a comment and is not read in The next line lists two numbers The first of these numbers gives the number of basis functions for that atom and basis set as listed in the default ba
384. need to run the Jaguar job you have just specified See Section 2 9 on page 22 for information on running jobs Jaguar 7 0 User Manual 139 Chapter 6 Using Jaguar 140 Making Input Files for GVB Calculations To set up the gau file for a GVB calculation you should specify the GVB pairs in the Theory tab See Section 3 6 on page 43 for information on setting up GVB calculations If you have selected a GVB calculation symmetry is automatically turned off and the gau file also specifies nosymm You might want to delete this setting from the gau file after it is produced The gau file also contains a Jaguar generated initial guess if you have selected a GVB calcu lation and notes that this trial wave function is to be used as an initial guess for the GAUSSIAN run guess cards If you have chosen to do an initial guess only calculation as described above the initial guess is generated from Jaguar s GVB initial guess routine Otherwise the initial guess provided in the gau file is the final wave function resulting from the Jaguar SCF calculation performed starting from the GVB initial guess Other Jaguar Options for the gau File You can use a Jaguar input file to run a Jaguar job which generates a gau file See Chapter 8 for a description of input files Selecting the Gaussian input file gau output option described above corresponds to setting the output keyword ip160 to 2 in the gen section of the input f
385. nel by clicking its Help button The Help panel is displayed with the appropriate topic selected 11 1 Problems Getting Started If you are having problems starting Maestro or submitting jobs read this section Your local system manager should have already installed Jaguar If the command SSCHRODINGER maestro amp does not work because the maestro command does not exist or if you get an error message regarding installation contact this person The exact wording of error messages you get when trying to run Jaguar might differ from the error messages described here depending on your hardware and X implementation Remember that your X server is either your workstation or the machine that acts as the server for your X terminal the display host is the workstation or terminal at which you are sitting and you are trying to start Jaguar as an X client on some machine not necessarily serving as your X server Some of the issues addressed here are standard X windows or UNIX issues and consulting your X and UNIX documentation may help Also you may be able to avoid repeatedly entering commands described in this section by including them in your login cshrc or other startup files in your home directory If you can start Maestro but you have problems submitting jobs skip to Section 11 1 4 on page 286 and Section 11 1 5 on page 287 11 1 4 The SCHRODINGER Environment Variable Before running Jaguar on any particular machine you must set
386. nents of the ECP and should begin with a line starting D_AND_UP F_AND_UP or G_AND_UP which indicates that the maximum angular momentum to be described is 2 3 or 4 Following that line the different terms for this angular projector are given Each line describes a term of the form Ce r 2 listing the parameters n ot and C from left to right in a free format Next the angular projectors are listed in increasing order S P D etc in the same fashion A line with four characters appears the end of the description of each atom s ECP When all atoms have been described in turn the next basis set is described The example below shows the beginning of the description in default basis of the LAV2D and LAV2P basis sets Note that these basis sets only differ in their choice of what basis set to use for atoms that are not described by the effective core potential BASIS LAV2D LANL1DZ 5D ECP BACKUP D95V BASIS LAV2P 5D ECP BACKUP 6 31G Na S 0 Lr 1 0 0 497200000000000 0 275357400000000 5 600000000000000E 02 1 09899690000000 S 0 T 0 2 210000000000000E 02 1 00000000000000 p 0 1 1 1 0 0 669700000000000 6 838450000000000E 02 6 360000000000000E 02 1 01405500000000 p 0 1 0 2 040000000000000E 02 1 00000000000000 kk Na 2 10 D_AND_UP 1 175 55025900 10 00000000 2 35 05167910 47 49020240 2 7 90602700 17 22830070 2 2 33657190 6 06377820 2 0 77998670 0 72993930 Jaguar 7 0 User Manual Chap
387. ngle point calculations Jobs that cannot be run in parallel mode include Jobs that use all analytic SCF methods LMP2 jobs other than closed shell single point calculations LMP2 jobs with more processors than LMP2 orbitals GVB and GVB LMP2 jobs CPHF hyper polarizability and NMR jobs Jobs using more processors than there are atoms in the input structure Jobs that use the Jaguar batch facility including pK jobs but see the end of Section 12 2 for exceptions 12 1 Installing Parallel Jaguar Parallel Jaguar is available for all supported platforms The parallel Jaguar executables are installed by default when you install Jaguar After installation the hosts on which you will run Jaguar may need to be configured for parallel execution Installation and configuration instruc tions are given in the Installation Guide and are repeated below In addition to host configuration the file SSCHRODINGER schrodinger hosts must be edited to add entries for the parallel hosts Each parallel host entry must include a processors line that indicates how many CPUs are available on that host This information is used in the GUI to display the maximum number of processors available for a host and to check that this limit is not exceeded For computer clusters that do not use queuing software an entry must be Jaguar 7 0 User Manual 291 Chapter 12 Parallel Jaguar 292 included for each node and the value of processors for
388. nly the output file and any other files you requested If you get an error related to temporary directory space when you try to run Jaguar the program is probably having trouble getting access to the temporary directory space it needs to run If you are using Maestro to run jobs you can tell what temporary space Jaguar will try to use by looking at the Scratch directory setting in the Start dialog box The program actually makes a subdirectory named after the job within this directory and writes files there For instance if a person with the user name erwin has a Scratch directory listing of scr for a job called n2o Jaguar attempts to create the directory scr erwin h2o and write files there during the job If your job gives error messages related to the temporary directory you should check to make sure that the temporary directory listed in the Start dialog box exists and that you have write permission within that directory For example if the output Error creating or cd ing to temp directory scr erwin h2o appeared in the bio Log file for erwin s job it could be because scr erwin did not exist or because erwin did not have permission to make the subdirectory h2o within it If you are running parallel or distributed jobs you might not have permission to create a directory on one of the hosts Jaguar 7 0 User Manual Chapter 11 Troubleshooting You might need someone to create the appropriate temporary directory or change perm
389. ns including Hessian refinement If you add an asterisk to a coordinate value Jaguar computes the gradient of the energy both at the original geometry and at a geometry for which the asterisk marked coordinate has been changed slightly and will use the results to refine the initial Hessian to be used for the optimi zation To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the zvar section line that defines the variables For instance a job that included Hessian refinement that was run with the following zmat section would use both O H bonds and the H O H angle in the refinement amp zmat O1 H2 O1 LH H3 O1 1 T H2 108 0 amp Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refine ment For instance for the water input example shown above only two coordinates will actu ally be refined the O H bond distance which is the same for both bonds and the H O H angle if molecular symmetry is used for the job Certain types of transition state optimizations require that you enter two or three geometries see Section 4 3 on page 74 for details For these jobs you can input the second and third geometries Geometry 2 and Geometry 3 in the zmat2 and zmat3 sections The order of atoms in the input must be the same as in the
390. ns from the exponents just given in the daf file for uncon Jaguar 7 0 User Manual 245 Chapter 9 Other Jaguar Files 246 tracted functions and already established in the basis file for contracted functions and contraction coefficients for contracted functions also established in the basis file If the value is 1 an s type function will be constructed using the relevant exponent or exponents if 2 a p type function if 4 a d type function if 8 an f type function and if 16 a g type function To construct more than one of these types of functions with the same exponent or exponents the relevant numbers should be added together for instance 1 2 4 7 for s p and d The exponent or exponents for each of these functions are determined by the position of the entry in the row The uncontracted functions are described first in the same order as their expo nents were listed earlier and the contracted functions corresponding to the contracted func tions found in the basis file are described next in the same order as in the basis set file Uncontracted functions in the basis set file should be ignored Finally the first derivatives of the basis set file contracted functions will be calculated and the values listed for these extra functions correspond to the functions generated this way in order of the function they were generated from and within that order of increasing complexity s before p etc For instanc
391. nt based methods Optimal use of the methodology in this fashion is accomplished by performing solution phase conformational searches with MacroModel Third the method can handle multiple protonation states in a systematic fashion This chapter is divided into four sections First the basic theory of pK calculations is explained including a discussion of the empirical correction approach Then a discussion of key issues in using the program in complex situations conformational flexibility multiple protonation states is given Thirdly results from our internal suite of test cases are presented Finally a practical tutorial describing how to set up run and interpret jobs is presented Jaguar 7 0 User Manual 303 Chapter 13 The pK Prediction Module 304 13 1 Theory of pK Calculation 13 1 1 Ab initio Quantum Chemical Calculation of pK Values The calculation of the pK of a molecule in aqueous solution can be represented as a thermody namic cycle A BH gt Bg H g p te BH aq gt Bag H vi The strategy in our pK module is to calculate parts A B and C of the above cycle whereupon the actual pK which is related to D by 1 PK yan can be obtained by summing the free energy changes for these three components and the experimental value of 259 5 kcal mol for the solvation free energy change of a proton Segment A is the gas phase reaction A DT 9 gt Bg Hei The
392. nverged gas phase wave function an additional free energy term that depends on the solvent accessible surface area SASA 164 of the molecular system and a set of empirical functions called atomic surface tensions The first solvation shell effects that are accounted for by this addi tional free energy term include but are not limited to cavitation dispersion interactions partial covalency of hydrogen bonds to the solvent and deviations of the dielectric constant of the solvent bath immediately surrounding the molecule from that of the pure solvent Since the atomic surface tensions are empirical they also make up to some extent for systematic errors in the theoretical model The computed solvation free energy from an SM6 calculation is for a temperature of 298 K and uses a standard state concentration of 1 M in both the gaseous and solution phases Solvation free energies in the literature are often tabulated using a standard state gas phase pressure of 1 atm To convert solvation free energies to a standard state that uses a gas phase pressure of 1 atm add 1 89 kcal mol to the computed solvation free energy Solution phase geometry optimizations cannot be carried out with SM6 As a result solvation free energies can only be computed using rigid geometries However because the parameters 72 Keyword nogas 0 in the gen section 73 Keyword nogas 2 in the gen section 74 Keyword nogas 1 in the gen section Jaguar 7 0 User Manual
393. nvi ronment variable inside the template sh script that is used to run the job See Section 6 3 2 3 of the Installation Guide for more information on this file Jaguar batch jobs cannot use MPI for the individual subjobs unless you make a special modifi cation to the batch script The batch variable FFLAGS may be set to PROCS 7 where is the number of processors to be used Without this modification if you request multiple processors for a batch job with multiple input structures or files the subjobs are distributed over the avail able processors with one job per processor This default behavior is generally more efficient for running batch jobs The FFLAGS modification should not be used if the batch job is to be submitted to a queue because in that case the queue would not know how many processors were to be allocated to that job If the number of jobs that you would like to run is greater than or equal to the number of processors available then the most efficient way to run them is to launch them all at once but use just one processor per job This is because parallelization is never 100 efficient Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module Schr dinger s pK prediction module represents the first attempt to use ab initio quantum chemical methods to reliably predict pK values in aqueous media 179 The module uses a combination of correlated ab initio quantum chemistry a self consistent reaction field SC
394. o a function on the grid can be better described using the dealiasing functions than by the basis functions alone The basis set coefficients for the function can then be determined by using the overlap between the dealiasing functions and the basis set functions which is deter mined analytically Some basis functions die off slowly and require long range functions centered on each atom in the molecule while others die off quickly over distance and can be described with short range dealiasing functions centered on the nearby atoms The latter type can employ different dealiasing functions depending on the distance between the atom upon which the relevant Jaguar 7 0 User Manual 243 Chapter 9 Other Jaguar Files 244 basis function is centered and the atom upon which the short range dealiasing functions are to be centered If the atoms are the same home atom dealiasing functions are used otherwise the distance between the two atoms determines whether the dealiasing functions used should be those for first order or one of the other higher order neighbors If the two atoms are further away than the farthest neighbor range specified no dealiasing functions on one atom are used in calculating the contribution of a short range basis function centered on the other atom The dealiasing functions themselves are simple polynomials multiplied by Gaussian functions and are s type p type and so on depending on the polynomial Uncontr
395. o the reactant geometry change this setting to a number between 0 and 0 5 to pick a guess closer to the product geometry set the Initial LST guess value to a number between 0 5 and 1 0 For the first few steps of a QST guided search the optimizer is restricted to searching along the circular curve connecting the reactant transition state guess and product structures This restriction prevents the optimizer from being led far astray by the inaccuracies of the guess Hessian and prevents it from exploring transition states that do not correspond to the reaction of interest During these steps the optimizer approaches the maximum energy structure along the reactant to product curve and also greatly improves the Hessian Once it has obtained the improved Hessian and transition state guess the optimizer removes the requirement that the search must be along the curve between the structures For all subse quent steps in the search the optimizer follows the Hessian eigenvector that is most similar to the tangent of the circular curve If no Hessian eigenvector is sufficiently similar to the tangent to the curve the optimizer follows the lowest eigenvector If you have a fairly good transition state guess but cannot provide reactant or product struc tures you can still use the standard non QST method This optimizer attempts at each step to maximize the energy along the lowest frequency eigenvector of the Hessian and to minimize along all othe
396. ollowing format where square brackets denote optional entries and entries in italics represent a character string with no spaces comments sections describing molecule amp calculation BASISFILE file path name basis ATOMIGFILE file path name atomig DAFFILE file path name daf GRIDFILE file path name gxid CUTOFFFILE file path name cutoff LEWISFILE file path name lewis GPTSFILE file path name The last six lines are only rarely used Therefore your Jaguar input files will generally take a form as simple as sections describing molecule amp calculation Jaguar 7 0 User Manual 155 Chapter 8 The Jaguar Input File 156 where only the zmat section which contains the geometry is actually required The basis atomig daf grid cutoff and lewis data files are described in Chapter 9 If you want to use non default choices for any of these files you can specify their paths and names on the appropriate lines of the input file If a file name ends with z for example BASISFILE erwin basis Z Jaguar copies the file and uncompresses it You can specify a file on another host or under another account name on that host by listing the file name in the format host fullpath or user amp host fullpath The GPTSFILE line allows you to use grid points and weights from an input file for any one grid used during the calculation The file should have a line for each
397. ols for selecting the structures that you must provide become available You can either type the entry name in the text box or click Choose to open an entry selector and select the entry To display any of these structures in the Workspace click the inclusion button to the left of the entry Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans name The diamond is checked when the structure is displayed Click the button again to undis play the structure The structures that you specify for the reaction must have the atoms listed in the same order One way of ensuring the correct ordering is to build one structure in Maestro then modify it to generate the other one or two For an example see the Jaguar Quick Start Guide If the atoms are not in the correct order you must edit the geometries to place them in the correct order For best results the reactant and product structures should not be radically different from the transition state For instance to find the transition state in a bond breaking reaction it would be better to provide a product structure in which the breaking bond was fairly long and weak than a true minimum energy structure in which the bond had completely dissociated The reactant and product structures are added to the zmat2 and zmat3 sections of the input file for QST searches and to the zmat and zmat2 sections for LST searches If you want to edit the structures you can do so in the Edit Job dialog box Wh
398. om the Jaguar run and whose name ends in gau can be used as a GAUSSIAN input file The gau file requests an HF or ROHF restricted open shell Hartree Fock calculation whichever is appropriate for the number of electrons in the system unless you choose to specify another method Details applying only to constructing an input file for a GVB calcula tion are discussed below To create a gau file select the Gaussian input file gau option in the Output tab If you are just creating a GAUSSIAN input file and you do not want to use Jaguar to generate a converged wave function you can save some time by choosing Initial Guess Only from the Jaguar submenu of the Applications menu or using the Edit Job dialog box to add the keyword setting igonly 1 initial guess only to the gen section of the input file The information in the gau file depends on the information you have provided The file always contains a molecular geometry in Cartesian coordinates and angstroms instructions for how to input geometries are available in Section 2 4 on page 9 The file also specifies the molecular charge and the spin multiplicity of the molecule If you want either of these values to be non zero you can make the appropriate settings in the Molecule tab You can also set the name of the basis set you want to provide in the gau file for example STO 3G using the Molecule tab The default basis set choice is 6 31G To actually generate the gau file you
399. ometry optimization step from the original geometry and the optimization continues until convergence For transition state optimizations the output for iterations that follow any Hessian refinement includes information identifying the transition vector used for that iteration This output includes the transition vector s eigenvalue and the stretches bends or torsions that are its most important components For any optimization iteration using level shifting after any relevant lines of geopt output described above some information on the computed level shift which may then be adjusted to satisfy step size constraints is included in the output For optimization steps past the first geometry change the change in total energy from the previous geometry to the newly calcu lated geometry in Hartrees is listed next The geopt output then lists the maximum element of the analytic gradient calculated by the earlier programs the root mean square of the gradient elements the step size predicted for the geometry change the trust radius for that iteration and if it is smaller than the step size the factor used to scale the step size so it is no larger than the trust radius the maximum element of nuclear displacement and the root mean square element of the nuclear displacement The predicted energy change for the new structure generated by geopt is also listed The values for the energy change gradient and nuclear displacement described in th
400. ommand and try again If the xauth command yields Permission denied the rsh command was not allowed and you should read the paragraphs on rsh and rcp commands in Section 11 1 5 on page 287 Jaguar 7 0 User Manual 285 Chapter 11 Troubleshooting 286 If you have problems running the xauth command described in the above paragraph an alter native is to simply type xhost ihost on your X server This command allows anyone including yourself logged onto ihost to run X programs on displayhost Since this command is a potential security risk it is not recom mended as a permanent solution If you are using an SGI and you get an error message like this dgl error getservbyname unknown service sgi dgl tcp it means Jaguar is unable to find the SGI Distributed Graphics Library The file etc services should contain this information in a line beginning sgi dgl If this line is commented out that is if it begins with a character you can try uncommenting it If you continue to have this problem and it is affecting the GUI performance you should ask your system administrator for help 11 1 4 Problems Related to Your Temporary Directory When you run a Jaguar job Jaguar generates various files it needs during the calculation within a temporary directory often within a directory called scr tmp or something similar At the end of the job the program deletes most files in this directory by default copying back o
401. oms are X or Du An example of the use of a dummy atom for CH4OH input follows C O C 1 421 Hl C 1 094 O 107 2 Xl CG 1 000 O 129 9 H1 180 0 H2 C 1 094 X1 54 25 H1 90 0 H3 1 094 X1 54 25 H1 90 0 H4 0 0 963 C 108 0 H1 180 0 Jaguar 7 0 User Manual 13 Chapter 2 Running Jaguar From Maestro 14 2 4 6 Constraining Z Matrix Bond Lengths or Angles To freeze bond lengths or angles during a geometry optimization add a sign after the coordi nate values For example to fix the HOH bond angle of water to be 106 0 you could enter the following Z matrix O H1 O 0 9428 H1 O 0 9428 H1 106 0 In a geometry optimization on this input geometry the bond angle remains frozen at 106 throughout the optimization although the bond lengths would vary For more details see Section 4 2 on page 70 which describes how to set up constraints for optimizations To constrain two geometric parameters to be the same during a geometry optimization use variables in Z matrix input see Section 2 4 5 on page 13 To freeze variables during an opti mization add a sign to the end of the variable setting in the variable definition section In this example the C H bond is frozen at 1 09 A chbond 1 09 HCHang 109 47 2 4 7 Counterpoise Calculations Following the procedure of Boys and Bernardi 29 a counterpoise calculation is often used to correct for the problem of basis set superposition error BSSE which arises when an incom
402. on tmig Jaguar generates a set of states with all possible d orbital occupations You can select one of these states by setting istate to the state Jaguar 7 0 User Manual 199 Chapter 8 The Jaguar Input File 200 index This capability is useful when there are degenerate states such as in highly symmetric transition metal complexes When degenerate states are encountered Jaguar prints a warning message that lists the states with a state index number and by default continues the calculation with the first state This calculation might not converge to the ground state so you should run calculations for each state to determine which is the desired state To run a calculation with another state set istate to the state index number listed in the output 8 5 19 Localization Keywords For any Jaguar job the final wave function can be localized after it is computed Localization can also be used to provide localized orbitals for the LMP2 method see Section 8 5 7 on page 167 for details The keywords in Table 8 30 describe the available options for final wave Table 8 30 Keywords related to localization of orbitals Keyword Value Description locpostc 0 Do not localize core orbitals of final wave function 1 Perform Boys localization on core orbitals of final wave function 2 Perform Pipek Mezey localization on core orbitals of final wave func tion maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on core
403. on type The element and chemical environment of each atom determine its atom type When Jaguar reads the Lewis file it sets the atom s van der Waals radius to the value dictated by the first atom type description in the Lewis file that matches that atom For instance if the atom were a methyl carbon and the first atom type description in the file was of a carbon bound to a hydrogen the radius would be Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files set to the radius matching that description even if a later line in the Lewis file described a carbon bound to three hydrogens Atom types are determined by an atom s element and by any combination of the following other properties Hybridization for example sp Bonding type which is determined by the bond orders of the bond s the atom forms and the element s to which the atom is bonded Hybridization type which describes the hybridization and element of atoms to which the original atom is bonded e Ring size the size of the ring the atom is in for instance 6 for a carbon in benzene Aromaticity of the ring the atom is in if any An aromatic ring is defined here by the Huckel Rule if the ring contains 4n 2 pi electrons where n is any non negative integer it is considered to be aromatic The Lewis file first determines the bonding types and hybridization types that will be recog nized then lists atomic radii for various atom types The file contains di
404. onstraining to reproduce multipole Moments 0 0 eee 53 54 for LMP2 wavefunctions 53 for solvation calculations 48 102 103 TIC LOR TEE 54 KEY Words iaceo tient ees 188 keywords for grid 188 212 Output from nes 110 111 recalculating multipole moments from 54 55 RMS error in out 110 setting options for ssssseseeersesieeererersesreee 52 energy components keyword for output of 208 energy convergence criterion ssss 46 keyword f r eienieeite etes 193 energy difference as geometry convergence criterion 69 101 keyword for geometry convergence 183 energy output final GVB components 98 final SCF components 96 SCF components for each iteration 208 GO 103 106 total SCF for each iteration 96 129 two electron contributions 120 enthalpy calculations 62 63 115 191 entropy calculations 62 63 115 191 environment variables DISPLAY HOME JAGUAR EXEC LD LIBRARY PATH MMSHARE MP HOSTFILE Jaguar 7 0 User Manual MP RMPOOL ss sssscsstescseiatvicivsssszsedsapiteacobeaniss 300 MPT PASSPORT ss ccssescisniteacabarieasicanene 296 299 MPI USEPASSPORT eene 296 299 PA RSHCOMMAND i c ecscscssssssesesesseeeseese
405. onverted and a warning is displayed The reason for discarding the entire basis set is that the ECP is not valid for molecular calculations if some projectors are removed from the ECP The script does not automatically distinguish polarization or diffuse functions from regular basis functions If polarization or diffuse functions are included in the basis set and you want to be able to select them by using or then you must edit the output from the script and add the appropriate data to mark the basis function as a polarization or a diffuse function as described on page 238 Otherwise Jaguar treats them as part of the standard basis set as it does for cc pVTZ for example Note Any basis sets you add will only be available for non pseudospectral calculations because they do not have associated grids and dealiasing functions 9 2 The Initial Guess Data File The file default atomig contains the results of Hartree Fock calculations on atoms for various basis sets By default the initial guess is constructed from wave functions in this file When the basis set to be used for the calculation is 6 31G MSV LAV2P LAV2D LAV3P LAV3D LACVP or LACVD or any variant of these sets involving polarization or diffusion functions such as 6 31G the initial guess is formed from wave functions obtained from atomic calculations in that basis set ignoring polarization and diffusion functions Therefore if you change the basis file you
406. optimization and the C1 C2 C3 C4 torsion You can specify a value after the sign separated by a space If this value is different from the current value of the coordinate according to the geometry it will be used as a dynamic constraint For example consider the following zmat section for water in which the distance between the two hydrogen atoms is 1 507 angstroms amp zmat h2 o 0 95 hi 105 Now suppose you want to optimize the geometry subject to the constraint that the distance between the hydrogen atoms is 2 0 Then you would add the following coord section amp coord hl h2 2 0 amp Jaguar 7 0 User Manual 161 Chapter 8 The Jaguar Input File 162 You can specify a variable after the sign separated by a space The values that the variable takes must be given in a zvar section The following example defines a variable HH as the distance between H1 and H2 amp coord H1 H2 4 HH amp For torsional dihedral angles you can fix the natural torsional angle by specifying the bond about which rotation can take place followed by nt or NT no spaces as in the following example amp coord C1 C2 isnt amp The natural torsional angle is the average of all the torsional angles that can be defined using this bond and the atoms bonded to either end of it The main use of the natural torsional angle is in coordinate scans where it permits an averaged torsional potential to be obtained See Sect
407. option with device ch_p4 If rsh is not allowed on your computer network then set RSHCOMMAND ssh in your environ ment before running the configure script The directory in which you installed MPICH is referred to below as MPICH_install Note If you use ssh instead of rsh you should set SCHRODINGER_RSH ssh in your shell startup script before launching Jaguar jobs so that Job Control also uses ssh 12 1 2 2 Configuration 1 Add the MPICH bin directory to the PATH environment variable This is necessary for Jaguar to find the mpirun launch script csh tcsh setenv PATH MPICH install bin PATH sh ksh bash export PATH MPICH_install bin PATH 2 If you plan to run Jaguar on a workstation or computer cluster that does not use any queueing software edit the file MPICH install share machines LINUX and list the names of the hosts available for parallel calculations Each host name should be listed once for each processor on that host The host name must match the output of the 3 Please see the notice regarding third party programs and third party Web sites on the copyright page at the front of this manual Jaguar 7 0 User Manual Chapter 12 Parallel Jaguar hostname command For example homer mynet edu homer mynet edu marge mynet edu marge mynet edu bart mynet edu Do not use the hostname ncpus syntax because this syntax requests the use of shared memory and Jaguar does not use shared memory for MPI calcul
408. or DFT calculations lastwv 0 Skip diagonalization of Fock matrix on last iteration 1 Diagonalize Fock matrix on last iteration nosuper 0 Evaluate integrals simultaneously over s and p basis functions with the same exponents superblocks 1 Evaluate integrals separately for s and p basis functions which have the same exponents 2 Use superblocks for all integrals except for gradient itwice 1 Do A integrals once in SCF routine 2 Do A integrals twice in SCF routine required for GVB optional for HF ichange z Change all cutoffs except those related to S eigenvalues bc pairs or ab distance cutoff for exchange by a factor of 10 to the ichange power dconv 5x10 SCF density convergence threshold RMS change in density matrix econv 5x10 SCF energy convergence threshold in hartrees maximum difference in energy between one SCF iteration and the next required for convergence Default is 1e 6 for polarizability and hyperpolarizability stdiis 100 0 DIIS initiation threshold DIIS is started when the largest value of the DIIS error vector is less than this value vshift 0 0 Level shift for virtual orbitals the amount the virtual orbital energies are increased before diagonalization in hartrees Default for pure DFT is 0 3 for hybrid DFT is 0 2 ifdtherm 0 Do not use thermal smearing in DFT or HF calculations 1 Use fractional occupation number FON method for thermal smearing 148 2 Use pseudo fra
409. orbitals of final wave func tion maximizing Mulliken basis function populations 1 Mix the core and valence orbitals before localization then localize according to the locpostv setting locpostv 0 Do not localize valence orbitals of final wave function 1 Perform Boys localization on valence orbitals of final wave function 2 Perform Pipek Mezey localization on valence orbitals of final wave function maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on valence orbitals of final wave function maximizing Mulliken basis function populations iordboy 0 Do not order orbitals at end of Boys localization 1 Order orbitals by their one electron energy at the end of Boys localiza tion ixtrboy 0 Do not try to diagonalize multiple bond orbitals at the end of the Boys localization 1 Try to diagonalize multiple bond orbitals at the end of the Boys local ization see text in this subsection Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File function localization See Section 3 8 4 on page 48 for a description of the localization methods and the GUI settings related to localization When the keyword ixtrboy described in Table 8 30 is set to 1 an additional procedure is added on to the Boys localization process Boys orbitals may be unphysical for multiple bonds since they create multiple banana bonds between pairs of atoms rather than forming sigma like pi like and related orbitals The Boys or
410. ormer that is found by the search algorithm is minimized using the selected force field Some minimizations may not converge within the limit of minimization steps This is not necessarily a problem but if you want to ensure that you only use fully mini mized structures as input to Jaguar there are two ways to do it The first is to simply increase the limit on the number of minimization steps while performing the conformational search However this can be expensive when large numbers of conformers are generated because you will probably refine only a subset of these with Jaguar If you expect the number of conformers to be large the second approach is to decrease the limit on the number of minimization steps while performing the search so that it finishes quickly After the search has finished and the results have been incorporated into the Project Table you can select a subset of them and mini mize them all using a MacroModel multiple minimization At this point you would use a high limit on the number of minimization steps to ensure that all minimizations converge After running the conformational search from Maestro the results are incorporated into the Project Table ranked so that the lowest energy structures are uppermost At this point you should examine the results and select an appropriate subset of conformers for refinement with Jaguar Then choose Optimization from the Jaguar submenu of the Applications menu At the top of the Jaguar pan
411. orrespond to that desired for the molecule the keyword lewstr should be changed to correspond to a better structure as described in Section 8 5 on page 163 To avoid using Lewis dot structures for either correction terms or radius settings set the gen section keyword isurf to 0 To use Lewis dot structures to set radii but not for correction terms isurf should be 0 but the keyword ivanset should be 1 All Lewis dot keywords are explained in Section 8 5 6 on page 165 The radius settings in the file default Lewis which appears in the standard data directory were optimized for HF GVB and LMP2 solvation calculations in water with Jaguar s solva tion module that included the default correction terms for the cavity and surface area The molecules used for radius optimization were the molecules containing carbon hydrogen oxygen nitrogen and sulfur from reference 155 AII calculations used a 6 31G basis set Geometries were obtained from gas phase optimizations at the HF GVB and LMP2 levels For both the geometry optimizations and the solvation energy calculations the GVB and LMP2 treatment was restricted to heteroatom pairs Jaguar 7 0 User Manual Chapter 10 Running Jobs Running monitoring and controlling jobs is done by the Schr dinger job control facility This facility has both a graphical user interface in the Maestro Monitor panel and a command line interface in the jobcontrol command The job control facility handles scra
412. ot have spaces around the or operators Host names cannot be included in any of the paths described in the table You should avoid using any of the charac ters lt gt in a substitution pattern Table 10 5 Definition of options that are applied to a template file to generate an input file Change Format Examples set keywords keyword new value or key basis lav3p word NONE to remove a setting dftname b3lyp igeopt NONE specify a data file path filetype fullpathname or file BASISFILE usr es my bas and name type NONE to return to default ATOMIGFILE NONE choice for that file type DAFFILE NONE GRIDFILE NONE CUTOFFFILE NONE GPTSFILE NONE WAVEFNFILE NONE remove a section RMSECTION section name RMSECTION guess RMSECTION gvb e z clear the gen section RESETGI except for the multip and molchg settings Jaguar 7 0 User Manual 275 Chapter 10 Running Jobs 276 Table 10 5 Definition of options that are applied to a template file to generate an input file Change Format Examples insert a file at the top of ADDTOP filename ADDTOP guess txt the input append a file to the ADDEND filename ADDEND guess txt input substitute a value for a old pattern new pattern bond 1 5 variable Do not use any of the characters torang 170 0 1 lt gt in either pattern a Filename must not end in in as this is taken as an input file These options and the other
413. ou can proceed to the rest of the chapter to learn how to input molecular structures and run jobs If you have problems starting Maestro or running the sample calculation see the troubleshooting information in Chapter 11 Chapters 3 and 4 describe the available calculation options which allow you to specify which properties you want the program to calculate and which methods you want it to use Chapter 3 includes information on using generalized valence bond GVB restricted configuration inter action RCI Mgller Plesset second order perturbation theory and density functional theory DFT techniques calculating solvation energies vibrational frequencies hyperpolarizabili ties multipole moments and other properties fitting charges specifying basis sets and various other options Chapter 4 describes optimizations of the molecular structure transition state searches and geometry scans Chapter 5 describes how to summarize Jaguar output and the output or printing options avail able from the GUI The output file containing the primary Jaguar output is first described for cases where no Output options have been selected Next the output given when various Output settings are turned on is explained Finally the log file is described Chapter 6 contains tips and suggestions for using Jaguar The chapter includes some general tips for different sorts of calculations a description of how to restart calculations how to incor porate results
414. out informa tion on the type of calculation to perform you can read them using the Jaguar Read dialog box which you open by clicking the Read button in the Jaguar panel This dialog box is a file selector with the usual file browsing tools a Filter text box a Directories list a Files list and a Selection text box By default information is displayed for the current working directory When you read a Jaguar input file you can read the geometry only or you can read the entire input file To read just the geometry choose Geometry only from the Read as option menu To read the entire input file choose Geometry and settings from the Read as option menu If you read in a geometry only from a file Jaguar also tries to obtain information on the molecular charge If you read the geometry and settings the settings are used to determine the Jaguar task which might not be the task with which you opened the Jaguar panel For example if you chose Single Point Energy then read an input file for a geometry optimization including the settings the task is reset to Optimization The structures in the input file are added as entries in the Project Table named with the stem of the input file name by default For example reading h20 in creates an entry named bio To read geometries from files generated or used by other programs you must import them into Maestro using the Import panel The files are imported using the file format conversion program Babe
415. owed to move only within the xy plane in which they started If frozen Cartesian coordinates are included in the input for an optimization Jaguar uses Carte sian coordinates for the optimization rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry 2 4 4 Z Matrix Format for Geometry Input Like Cartesian geometries Z matrix format geometries also specify atoms by atom labels that begin with the one or two letter element symbol The atom label is case insensitive The element symbol may be followed by additional characters as long as the atom label has eight or fewer characters and the element symbol is still clear The first line of the Z matrix should contain only one item the atom label for the first atom For example N1 This atom is placed at the origin The second line contains the atom label for atom 2 the iden tifier of atom 1 and the distance between atoms 1 and 2 Identifiers can either be atom labels or atom numbers the position in the list 1 for the first atom 5 for the fifth atom listed and so on In this example the identifier for the first atom could be either N1 or 1 The second atom is placed along the positive z axis For example N1 C2 N1 1 4589 Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro 12 places the carbon atom C2 at 0 0 0 0 1 4589 in Cartesian coordinates Distances between atoms must be posi
416. own in Table 8 21 may be used to specify the geometry convergence criteria or these criteria may be scaled to five times their default values with the keyword setting iaccg 3 for a quicker coarser calculation The first four keywords listed in Table 8 21 have units of hartrees bohr gconv5 and gconv6 have units of bohrs and gconv7 has units of hartrees SCF calculations performed for each new structure generated during an optimization are judged to be converged when they meet the criterion for the root mean square of the change in density matrix elements which is controlled by the keyword dconv the usual SCF energy convergence criterion econv is ignored for optimizations If you want to save the structure at each step of a geometry optimization in a Maestro formatted file set ip472 2 You can also extract the structures from the output file to a Maestro file with the command jaguar babel ijagout jobname out omacmod filename mae Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File If you import the structures into Maestro you should set the color scheme manually it is not set correctly on import Table 8 21 Geometry convergence criteria keywords Keyword Default value Convergence Criterion For gconvl 4 5x104 Maximum element of gradient gconv2 3 0x10 rms of gradient elements gconv3 1 0x10 Maximum Newton Raphson step not currently used gconv4 1 0x107 rms Newton Raphson step not cu
417. own in Table 8 5 describe how the program uses symmetry Table 8 5 Symmetry related keywords in Jaguar Keyword Value Description isymm 0 Do not use symmetry 1 Rotate atomic grids to match molecular symmetry if possible 2 Change grids to get molecular symmetry if necessary 8 Use symmetry in preprocessing and SCF ipopsym 0 Allow change in number of electrons in each irreducible representa tion default for HF and DFT closed shell jobs 1 Don t allow number of electrons in each irreducible representation to change default for non HF non DFT and open shell calculations idoabe 0 Allow non Abelian point group symmetry assignment 1 Allow only Abelian point group symmetry assignment 8 5 6 GVB and Lewis Dot Structure Keywords The ihfgvb keyword allows you to specify the initial guess to be used for a generalized valence bond GVB calculation By default ihfgvb is set to 0 The ihfgvb keyword is described in Section 8 5 18 on page 198 Jaguar 7 0 User Manual 165 Chapter 8 The Jaguar Input File 166 GVB pairs are set in the gvb section where pairs to be used in an RCI restricted configuration interaction calculation are also specified and a GVB calculation will be performed any time one or more GVB pairs are described in the input file This includes the use of the igvball keyword You can find Lewis dot structures by setting the appropriate keywords and you can also use one of these structures to set GVB pair
418. pK values are well separated and the pK of site 1 is higher than that of site 2 In this case site 2 will be deprotonated when site 1 is being titrated in an experiment The pK calculation for site 1 is run with site 2 in the deprotonated state 2 The two pK values are well separated and the pK of site 2 is higher than that of site 1 In this case site 2 will be protonated when site 1 is being titrated in an experiment The pK calculation for site 1 is run with site 2 in the protonated state 3 The two pK values are unknown or the pK values are close together In this case there are a total of four protonation states to run both sites protonated one site protonated two cases and no sites protonated If one obtains data for these four cases the titration curve can be assembled and one can make comparison with experiment Cases 1 and 2 are straightforward to handle When the ionizable groups are close together in the molecule the calculated pK may not be as accurate because the two groups could interact in ways that the existing parameterization cannot handle For case 3 you must run two separate pK jobs each of which handles two of the four protonation states and build the titration curve by hand 13 3 Training Set Results Table 13 1 presents a summary of the results for the functional groups for which parameters are available including the average and maximum deviation from experiment The functional groups are clas
419. pdating iterations in the final sequence respectively Finally the last column dictates the cutoff sets used for non SCF calculations as for gradient calculations Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files The first six lines of the default cutoff file which illustrate these points are cutv0300 11117 max accuracy prelim prelim update final final update gradient 3 7 accurate 56268 quick solvent 00000 00000 The rest of the cutoff file consists of the cutoff sets Each set is specified by one line with four integers sometimes followed by lines containing explicit cutoff keyword values and ending with a blank line The four integers represent the variables jcor and kcor described below the grid number and the number of cutoff values to follow immediately below The grid number should be 1 for the coarse grid 2 for the medium grid 3 for the fine grid and 4 for the ultrafine grid 5 for the charge grid 6 for the gradient grid 7 for the electron density cubic grid 8 for the DFT medium grid or 10 for the DFT gradient grid where these grids are speci fied by the keywords gcoarse gmedium gfine gufine gcharge ggrad geldens gdftmed and gdftgrad Section 8 5 25 on page 210 contains more information on these keywords The next lines specify each cutoff by number e g 22 for the variable cut22 and value Thus the cutoff set 52423 set 3 21 1 0e 3 22 3 0 24 1 0e 2 means that jcor is 5 kcor
420. performed at the Quick accuracy level described in Section 3 8 1 on page 45 unless the input contains a transition metal in which case the accuracy level is Accurate However for the last few geometry iterations the accuracy level for the SCF calculations is reset to the Accurate level which uses tighter cutoffs and denser pseudospectral grids than the Quick level For optimizations to minimum energy structures or transition states the convergence criterion for SCF calculations is chosen to assure accurate analytic gradients For these jobs a wave Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans function is considered converged when the root mean squared RMS change in density matrix elements is less than the RMS density matrix element change criterion whose default value is 5 0 x 10 The SCF calculations during an optimization to a minimum energy structure or transition state do not use the energy convergence criterion used by other SCF calculations The RMS density matrix element criterion may be set in the SCF tab The geometry is considered to have converged when the energy of successive geometries and the elements of the analytic gradient of the energy and the displacement have met the conver gence criteria These criteria are all affected by the choices in the Convergence criteria section Default or Loose the loose criteria are all five times larger than the default criteria For opti mizations in solution the d
421. plete basis set is used in the calculation of the binding energy of a complex consisting of two or more molecules The calculation of a counterpoise corrected binding energy for a dimeric complex actually consists of seven calculations Geometry optimization of the complex calculation 1 Geometry optimization of each of the two molecular fragments in their own basis sets calculations 2 3 Single point calculations of each of the fragments in their own basis sets at the geome tries that they adopt in the complex calculations 4 5 Single point counterpoise calculations on each fragment at the geometries that they adopt in the complex using the basis set of the complex calculations 6 7 The usual uncorrected binding energy would be calculated as AE bing Ej E5 3 Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro where the energy subscripts refer to the calculations listed above The counterpoise correction to the binding energy expresses the artificial gain in energy of each molecular fragment when it can use the basis functions of the other fragment in addition to its own basis functions AE E4 Eg E Ey Calculated in this way the counterpoise correction is a positive number and it is added to AEF bing to yield the final binding energy Counterpoise corrections are often several kilocalo ries per mole in magnitude and decrease as the size of the basis set increases In the input
422. ponding neutral species due to the phenomenon of electrostriction In our fitting procedure the ionic radii are adjusted to yield the smoothest and most consistent results for the members of the training set for each functional group For anions special radii are assigned to the principal location of the negative charge for cations radii are assigned to hydrogens on the proton acceptor and to the proton acceptor itself Functional groups for which radii have been developed are listed in Table 13 1 on page 310 For novel functional groups with divergent electronic properties reparameterization of the model to a subset of experimental data is advisable as the results are rather sensitive to these quantities However the current model is able to robustly handle substituent and conformational effects once a func tional group is parameterized In our work on neutral solvation we have found that it is necessary to supplement parameter ization of dielectric radii with surface area terms to correct for first shell hydrogen bonding A purely electrostatic model is incapable by itself of properly describing such interactions for all molecules For ions these terms are expected to be even larger and more important as the magnitude of the first shell hydrogen bonding interactions are 3 5 times larger than in neutral species However what we have done in the present model is to incorporate these corrections into our overall empirical fitting scheme descr
423. possible to launch the daemons manually using the command SSCHRODINGER utilities mpich start p port If p port is not specified the value of MPI_P4SSPORT is used for the port number If MPI_P4SSPORT is not set the default value of 1234 is used The mpich script can be used to manage the secure servers The syntax for the script is SSCHRODINGER utilities mpich command options The available commands are listed in Table 12 1 and the available options are listed in Table 12 2 This script allows you to start and stop the servers on all or some of your machines and to check on their status through a single consistent interface The command acts on the hosts specified with the h option if any are given Otherwise it acts on the hosts listed in the machines file By default this file is the machines LINUX file from your MPICH installation or SCHRODINGER NODEFILE if it is set The port on which the servers listen can be specified using the p option or the MPI PASSPORT environment variable otherwise the standard port number 1234 is used Table 12 1 Commands for the mpich script Command Action start Start servers stop Kill servers restart Kill and restart servers status Report server status pid Report server PID sems Report semaphore sets in use rmsems Delete all semaphore sets shm Report shared memory segments in use rmshm Delete shared memory segments see text below rmipcs Delete both semaphores
424. pt by choosing Jaguar batch script from the File Format option menu When you click OK a Jaguar batch script is created that contains settings gen section and batch commands but no geometry so that you can run this script with any geometry To make use of this script you can select Run Batch File from the Jaguar submenu of the Applications menu in the main window You can also use Maestro to export structures to a variety of formats using the Babel file conversion program see Section 10 1 5 on page 269 See Chapter 3 of the Maestro User Manual for more information on exporting structures Jaguar 7 0 User Manual 21 Chapter 2 Running Jaguar From Maestro 22 2 9 Running Jobs Maestro provides several ways of running Jaguar jobs You can select a task from the Jaguar submenu of the Applications menu make settings then start the job you can select a set of preexisting input files and run them as a single job by selecting Run Input Files from the Jaguar submenu or you can run a job using a preexisting Jaguar batch file with one or more structures as input by selecting Run Batch File from the Jaguar submenu Whenever you run a calculation with multiple structures as input that does not have any geometry dependent settings a Jaguar batch script is created to run the calculation on each structure You can submit a job either from Maestro or from the command line Information on submit ting jobs from the command line with the ja
425. ption corresponds to an atom in a ring of size n or smaller unless the fifth integer is 1 in which case the question of the atom s ring environment is ignored completely The size n should not be more than 20 The sixth integer indicates whether the description corresponds to an atom in an aromatic ring as defined by the Huckel Rule 4n 2 electrons in ring where n is a non negative integer If the sixth integer is 1 the description corresponds to an aromatic ring if it is 0 the description corresponds to a non aromatic ring and if it is 1 the aromaticity of the ring is irrelevant Note however that aromaticity is not evaluated if the fifth integer describing ring size is 1 To describe aromaticity without regard to ring size you should generally set the fifth integer to 20 and the sixth to 1 corresponding to atoms in aromatic rings of size 20 or less 9 6 4 Default Behavior for Setting Radii The radius settings contained in Jaguar s default Lewis file are used for any relevant atoms in all default solvation calculations in water with Jaguar s solvation module except for calcula tions on ions or on molecules containing atoms with atomic numbers greater than 18 By default the program uses the first Lewis dot structure generated to evaluate the radii and the solvation calculation also includes a correction term the first shell correction factor that depends on that Lewis dot structure If the Lewis dot structure does not c
426. put froma PBF CalceulatiOni 5 sscacechesasecessasebcesgs srcateteaiaceas 5 3 5 2 Output from an SM6 Calculation 5 4 5 5 5 6 5 7 5 3 6 Geometry Optimization in Solution 5 3 7 ee EE 5 3 7 1 Multipole Moments and Charge Fitting 5 3 7 2 Polarizabilities and Hyperpolarizabilitios c sssecccccceeesesssesessesseees 5 3 7 3 Electron Denisily ee dd 5 3 7 4 Mulliken Populations seeni eaoaai ee EE 5 3 8 Frequency IR Intensity and Thermochemistry Output 114 5 3 9 CIS Cal tfe 116 5 9 10 Basis Sele ERI PITE 117 e a R E eTo E E lictor hi lUi EU uite 120 Options for Extra e LEE 121 File ee TT 124 Output Options for el TT 125 The Log File Rn 128 Jaguar 7 0 User Manual Contents Chapter 6 Using Ae eier oci dncicetidas 131 6 1 Choosing an Initial Guess s sees 131 CDN Daf e pL 131 61 2 GVB TEE 132 6 1 3 Initial Guess for Molecules Containing Transition Metals 133 6 2 SCF Convergence en dpi HELL esee LI EE i Res Hee acp ae 134 6 3 Geometry Optimization AA 135 6 4 Setting Up GVB Calculations AA 136 6 5 Restarting Jobs and Using Previous Results 136 6 6 Conformational Searches sse 138 6 7 Generating Input Files for GAUSSIAN senes 139 Chapter Seeerei 141 7 1 The Pseudospectral Method sse 141 7 2 Pseudospectral Implementation of the GVB Method
427. r 9 1 The Basis Set File The basis sets available for use in Jaguar appear in the file default basis in the standard data directories Portions of this file are shown in this section you might want to refer to them as you read the description of the file Basis sets at the top of the file do not contain effective core potentials and will be described first The basis sets with effective core potentials whose names begin with LA will be described later 9 1 1 Basis Set Format Each basis set description begins with a blank line The next line or lines must begin with the word BASIS followed by one space That label is followed by one or more names of the basis set to be described the name of the basis set as given in Table 3 1 on page 32 or Table 3 2 on page 34 and any other names which describe the same basis set eg STO 3G and STO3G The basis set names are separated by commas and must include and or characters if those Jaguar 7 0 User Manual 237 Chapter 9 Other Jaguar Files 238 are allowed for that basis set or character strings are sufficient to describe the and cases also and the characters can be listed either before or after the characters The next notation in the line SD or 6D sets the default number of functions for d shells when using that basis set as described in Section 3 2 on page 30 Backup basis set names which are each preceded by the word BACKUP m
428. r 1981 local functional 39 Perdew 1986 gradient cor rection functional 40 e BP86 VWN5 Exchange Slater local functional 34 Becke 1988 nonlocal gradient cor rection 37 correlation Vosko Wilk Nusair VWN local functional 35 Perdew 1986 gradient correction functional 40 10 Keyword dftname hfs in the gen section 11 Keyword dftname xalpha in the gen section 12 Keyword dftname svwn in the gen section 13 Keyword dftname svwnS in the gen section 14 Keyword dftname blyp in the gen section 15 Keyword dftname bpw91 in the gen section 16 Keyword dftname bp86 in the gen section 17 Keyword dftname bp86 vwn5 in the gen section Jaguar 7 0 User Manual 37 Chapter 3 Options 38 PWPW91 8 Exchange Slater local functional 34 Perdew Wang 1991 gradient correc tion functional 36 correlation Perdew Wang 1991 GGA II local and nonlocal func tionals 36 PRETT Perdew Burke Ernzerhof local and nonlocal exchange and correlation functional 47 HCTH407 Hamprecht Cohen Tozer Handy functional including local and nonlocal exchange and correlation reparametrized with a training set of 407 molecules by Boese and Handy 46 MO6 L Parameterization by Zhao and Truhlar of various functionals that include gradi ent and kinetic energy spin density functionals 54 Hybrid Functionals 18 19 20 21 22 23 24 25 26 27 28 B3LYP Exchange exact HF Slater loc
429. r coordinates This process is well defined and straightforward when the Hessian has exactly one negative frequency indicating that the structure is near a saddle point The negative eigenvalue mode which is sometimes known as the reaction coordinate is referred to as the transition vector in this chapter 17 Keyword iqst 0 in the gen section 18 Keyword iqst 1 in the gen section 19 Keyword qstinit in the gen section Jaguar 7 0 User Manual 75 Chapter 4 Optimizations and Scans 76 Jaguar jaguar DIE S Molecule Theory scr Optimization Transition State Properties Solvation Output Search method w Standard 4 LST v GST Structures Choose Choose Reactant Product Initial LST guess 0 50 Search along Reactant product path Follow same eigenvector o a W Hessian refinement Low frequency modes 1 Start Read Write Edit Reset Close Help Figure 4 2 The Transition State tab 4 3 2 Specifying Structures for the Reaction Structure selection for transition state searches operates differently from structure selection for other tasks The controls at the top of the Jaguar panel are not available Instead you select structures for the reaction from the entries in the Project Table using the controls in the Struc tures section of the Transition State tab When you choose a search method the contr
430. r molecule The sample calculation runs only if Jaguar has been correctly installed If the calculation does not run try the suggestions in Chapter 11 or see your system manager or the person who installed Jaguar at your site Contact Schr dinger if you cannot resolve the installation problems First log on to a machine where the Maestro and Jaguar software is installed Change to the directory where you want the Jaguar output files for the sample job to be written then start Maestro by entering the command Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro SSCHRODINGER maestro amp If SSCHRODINGER is in your PATH environment variable you can simply type maestro Once Maestro is running choose Single Point Energy from the Jaguar submenu of the Applications menu to open the Jaguar panel for a single point energy calculation see Figure 2 1 on page 7 The next step is to enter a molecular geometry structure You can enter the structure by hand or read it from a file To enter the structure by hand you can use the Edit Job window Click the Edit button select the Structure option then click in the text area and type the following lines 0 0 0 0 0 0 1135016 H1 0 753108 0 0 0 4540064 H2 0 753108 0 0 0 4540064 The labels begin with element symbols O and H The numerals 1 and 2 appended to the hydrogen labels distinguish between the atoms The next three numbers on each line give the x y and z Cartesian
431. r simultaneous accuracy of bond ener gies barrier heights and nonbonded interactions by Zhao and Truhlar 51 pw6b95 Reoptimization of MPW1B95 functional for simultaneous accuracy of bond ener gies barrier heights and nonbonded interactions by Zhao and Truhlar 51 m05 Hybrid functional parametrized for broad accuracy including noncovalent interac tions kinetics and interactions with metals by Zhao Schultz and Truhlar 52 53 m05 2x Hybrid functional with larger HF exchange component similar to M05 but param etrized for nonmetals by Zhao Schultz and Truhlar 52 53 m06 Zhao and Truhlar functional 56 m06 2x Zhao and Truhlar functional 56 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 8 Standard functional names for the dftname keyword Continued Name Description m06 1 Zhao and Truhlar gradient corrected functional 54 m06 hf Zhao and Truhlar functional 55 x3lyp Extension of B3LYP by Xu and Goddard to include Perdew Wang 1991 gradient correction exchange functional 36 with exchange parametrized to fit Gaussian exchange density 50 If you choose to use the idft keyword you can construct a combined functional from the avail able local and nonlocal exchange and correlation functionals Positive values of idft describe both the exchange and correlation functionals The value of idft can be broken down in the form idft 10000 i 1000 j 100 k 10 I m or idft ijklm w
432. r the cleanup minimization are deliberately set fairly loose so that even fairly large systems can be optimized interactively The practical size limit is about 300 atoms In addition a time limit is imposed on the minimization to keep it from running exces sively long As a result you might find that the geometry continues to change if you perform a second cleanup minimization on a cleaned up structure UFF cleanup minimization is useful for quickly bringing a distorted molecule back into the neighborhood of the ab initio minimum energy geometry in preparation for full ab initio geometry optimization However it is no substitute for ab initio optimization because UFF is a relatively simple force field It is probably a good idea to perform a cleanup minimization after creating a new molecule in the Build panel On the other hand performing a cleanup minimiza tion on a molecule that has already undergone ab initio minimization is likely to move the molecule away from the ab initio minimum Also you should be careful to avoid cleaning up a structure that has been prepared as an initial guess for a transition state search 2 7 2 Symmetrization By default Jaguar takes advantage of molecular symmetry whenever possible in order to save CPU time Both Abelian and non Abelian point groups are recognized Generally you should symmetrize the geometry if you plan to use symmetry in the calculation itself Otherwise the input coordinates may not be a
433. r transition metal containing systems which is based upon ligand field theory As described in Ref 21 research at Schr dinger has established that poor convergence of these systems is very often due to problems with the trial wave function s orbital shapes and occupa tions This initial guess method takes advantage of user provided information on charges and spins of fragments within the system as described in Section 6 1 3 on page 133 although such 1 Keyword iguess 10 in the gen section 2 Keyword iguess 0 in the gen section 3 Keyword iguess 11 in the gen section Jaguar 7 0 User Manual 131 Chapter 6 Using Jaguar 132 information is not required If you have an antiferromagnetic system this algorithm does not work but you can set keywords to ensure that you have the correct guess See Section 6 1 3 on page 133 for details You can also consider performing a calculation on a related system for which you can more easily obtain convergence for example one that is ionized and then use the results of this system as an initial guess for the system of interest When you restart a calculation with an input file generated during a previous run the wave function from the earlier run is read from the guess section and used as an initial guess The guess section is described in Section 8 10 on page 229 Jaguar can read in an initial guess in one basis set and transform it to the basis set requested for the calculation unl
434. rated because the Workspace contains a Scratch entry Would you like to make this entry a real entry run with a Scratch entry or cancel Create Entry Run With Scratch Cancel Figure 2 7 Scratch entry alert box If your job input is a scratch entry an alert box Figure 2 7 is displayed when you click Start before the Start dialog box is displayed This box prompts you to create a named entry from the scratch entry If you then click Run With Scratch Do not incorporate is automatically selected in the Start dialog box and the Incorporate controls are unavailable The job can be run but it cannot be incorporated into the project The local directory where input and output files created by Jaguar are written is determined by the setting in the Directory tab of the Preferences panel The default local job directory is the directory from which you read the input file if you read one or the directory you were in when you started Maestro See page 29 of the Maestro Overview for more information 2 9 2 Job Submission Options In the Job section you can provide a job name select the execution host the number of processors and the scratch directory The choices available in the Job section depend on the schrodinger hosts configuration file See Section 2 1 of the Job Control Guide for more information on this file The job name can be entered in the Name text box If the structure you are using for input is a named entry in the Projec
435. rbate fragments and cluster fragments For example for ferrocene the iron atom is one fragment and the two cyclopentadieny ligands are two additional fragments To supply Jaguar with information on charges and spins for its high quality initial guess for a transition metal containing system you need to edit the input file either from the Edit Job dialog box which you open by clicking the Edit button or from a terminal window First add the following lines to the bottom of the input file amp atomic atom formal multip amp The exact number of spaces between words does not matter Fill in information for each fragment under the headings atom formal and multip You should add a single line for each fragment with a formal charge or a non singlet spin multi plicity The first entry in the line under the heading atom should be the atom label of any atom in the fragment The next entry under the heading formal and separated from the first entry by one or more spaces should be the formal charge of the entire fragment The third entry under the heading multip should be the spin multiplicity of the fragment If C1 is in one ring of ferrocene and C6 is in the other ring then the following atomic section could be used to help generate the initial guess atom formal multip Fe 2 1 Cl 1 1 C6 e 1 amp Fragments with no formal charge and singlet spin water for example do not need to be listed in the atomic section because Ja
436. rder to avoid changing the geometry too much because of an unusually shaped potential well or an inaccuracy in the Hessian Jaguar restricts the norm of the changes to the Cartesian or internal coordinates to be less than a certain trust radius which is defined in atomic units bohrs and or radians The trust radius can vary from one iteration to another itradj 1 or it can be fixed itradj 0 Keywords controlling the use of a trust radius are listed in Table 8 20 If the trust radius is fixed it remains the same throughout the optimization except when Jaguar determines that changing it will lead to better convergence for problem jobs This setting is the default for optimizations to minimum energy structures If the trust radius is allowed to vary the default for transition state optimizations Jaguar keeps geometry changes within the region that is well described by the Hessian by increasing the trust radius when the Hessian is correctly predicting energy changes and decreasing it when the predictions are inaccurate Table 8 20 Keywords for trust radius adjustment Keyword Value Description itradj 0 Use same trust radius throughout optimization default for minimum energy structure optimizations 1 Adjust trust radius using Culot Fletcher heuristic 143 145 default for transition state optimizations 1 Adjust trust radius using Simons cubic potential model 146 not rec ommended with Jaguar itrcut 0 Apply trust radius by trun
437. rdinate scan you set up an input file with the coordinates defined as variables and the variable values defined as described below For a relaxed scan the job must be a geometry optimization for a rigid scan it must be an energy calculation You can define a variable in the geometry input as described in Section 2 4 5 on page 13 or you can define variables in the coord section Using the coord section allows you to define variables that are not part of the Z matrix geometry input To define a variable in the coord section add the variable name after the sign in the coordinate definition For example the following input file section defines a coordinate HH as the distance between H1 and H2 amp coord H1 H2 4 HH amp The values taken by a variable are defined in a zvar section To specify the values that a variable will take in a scan you can assign a list of values to the variable in the format at number list or you can assign the initial value specified by either number or rom number and two specifications from the following list in the order given in the list tonumber specify the final value of the coordinate by number specify the step size ininteger specify the number of steps Here integer means an appropriate integer and number means an appropriate real number If you specify the initial and final values they are always among the values set For example varying a coordinate from 0 to 120 by a step size o
438. rgy surface They are mainly used to check that the given transi tion state is indeed the expected transition state for the reaction of interest The keywords for IRC and MEP calculations are listed in Table 8 23 The forward and reverse directions are defined as follows The first set of conditions that constitutes a valid definition is used 1 If two additional geometries are entered in the zmat2 and zmat3 sections they are assumed to be the geometries for the reactant in zmat2 and product in zmat3 The for ward direction is defined as moving from reactant to product 2 If a vector is entered in the tvec section it defines the forward direction An example of such a vector is as follows amp tvec C2 H3 0 5 O1 C2 H3 1 0 amp This definition produces a composite coordinate that is the sum of 0 5 times the distance between atoms C2 and H3 and 1 0 times the angle O1 C2 H3 Coordinates comprising this composite can be any combination of bond stretches 2 atoms listed angle bends 3 atoms and dihedral angles or torsions 4 atoms Atom labels or index numbers for the atoms can be used in specifying atoms Coordinate coeffi cients specified by including an asterisk followed by a value after the last atom are optional The default coefficient value is 1 0 The forward direction is the direction that makes the composite coordinate defined in this section larger 3 The Hessian eigenvector for the imaginary freq
439. rimitive Gaussian If the linear combination has only one Gaussian primitive the function is called uncontracted otherwise it is called a contracted Gaussian Each shell is defined by a product of a polynomial and a Gaussian primitive Jaguar 7 0 User Manual 117 Chapter 5 Output 118 The shell information table is printed first An example for water with a 6 31G basis set is given below The first column indicates which atom the shell is centered on The second column lists the shell numbers which increase consecutively for each atom The values in the third column mean different things depending on their sign The positive numbers mean that the basis function currently being described is composed of that number of primitive Gauss ians starting with the primitive Gaussian for that row and including the appropriate number of rows immediately below it The negative numbers magnitudes indicate the first shell which contributes to the same contracted Gaussian function In the example below the first row has a jcont value of 6 indicating that the first basis function being described is a contracted Gaussian composed of that primitive Gaussian and the primitives in the next five rows The jcont values of 1 in the next five rows indicate that the primitive Gaussians being described are compo nents in a contracted function whose first primitive Gaussian term is listed in the first row The values in the column marked ishl ta
440. riting them to the output file as described above These force results are followed by the output from the program geopt which includes a number indicating how many times it has been called in the start of program geopt line Every time geopt is called this number is updated However since geopt can be called for Hessian refinement steps as well as for generating new geometries during an optimization and since geometry optimizations occasionally revert back to a previous geometry and restart the calculation from there the next line of the geopt output reports what sort of step is being performed and numbers that step accordingly If the program detects that the input lists separate fragments each of which contain only atoms unbonded to the atoms in any other fragment as for a van der Waals complex then the number of fragments is listed near the start of the geopt output For transition state optimizations the eigenvalues of the nuclear Hessian are reported the first time geopt runs If the initial Hessian is being refined the coordinates for the refinement and their eigenvalues are listed If a coordinate you have specified is inappropriate because of symmetry restrictions or other constraints the output will indicate the problem The geopt output then lists information on the current original geometry s gradient elements describes the small step it will use to alter the first coordinate used in the Hessian refinement de
441. rmined by the CUTOFFFILE entry in the input file as described in Section 8 1 on page 155 If the input file has no such entry Jaguar uses the file default cutoff from the data directory If the CUTOFFFILE entry is accurate cutoff solvent cutoff or quick cutoff the program interprets the setting as default cutoff The first line of a cutoff file contains a character string that includes the version number of Jaguar This should be cutv followed by four digits giving the version number times 100 Leading zeroes are added if necessary A comment on the same line can follow the version string The next five lines each have five numbers Each line describes a particular level of accuracy to be used for the calculation The first line provides the information necessary to run a calcula tion with all ultrafine pseudospectral grids and with tight cutoffs and corresponds to an accuracy level setting of Ultrafine from the GUI as described in Section 3 8 1 on page 45 or to the keyword setting iacc 1 in the gen section of the input file as described in Section 8 5 17 on page 193 The second line gives the parameters for the accurate level iacc 2 while the third line provides information for the quick level iacc 3 The last two lines are filled with Zeroes since they are required but are not yet used In each of these rows the columns describe which cutoff sets are used for various SCF itera tions The cutoff sets themselves are prov
442. rocessor in that node For example if you have a work station called bobcat with four processors and you want to be able to use all four processors the host file should contain the following four lines bobcat bobcat bobcat bobcat If you call this host file my host file then you should set MP_HOSTFILE as follows csh tcsh setenv MP HOSTFILE home userid my hostfile sh ksh bash export MP HOSTFILE home userid my hostfile If you are unsure of your system configuration contact your system administrator Ensure that the schrodinger hosts file is properly configured for your cluster See the Job Control Guide for more information on this file Finally you must also make sure you have rsh access to the host even if you are on it To do this add a line to your rhosts file that specifies the node that you need access to and your login name bobcat schrodinger com username This gives user username rsh access to host bobcat schrodinger com 12 2 Running Jobs in Parallel To run Jaguar jobs in parallel you need only specify the number of processors to use for the job at the time you launch it You do not need to launch mpirun or poe this is done automati cally by Jaguar If you launch the job from the command line set the PROCS option to the number of processors to be used For example jaguar run PROCS 8 HOST mysmp jobname If you launch the job from the GUI type the number of processors to be used
443. rom Workspace included entries Molecule Theory scr Optimization Scan Properties Solvation Output Add new coordinate Type Distance 1 F Pick Atoms 1 Defined coordinates maximum of 5 Selected coordinate Le et Distance 1 ES Current value 1 419 Starting value 0 00 7 Final value 0 00 Total number of structures to be calculated 1 Increment 0 000 Number of steps 1 Delete Start Read Write Edit Reset Close Help Figure 4 3 The Scan tab The Defined coordinates table displays information on the scan coordinates the definition the type and the number of steps The total number of structures to be calculated is reported below the table and is the product of the numbers in the Steps column To set the values for the coordinate select the row for the coordinate in the table then enter the starting value the final value and the increment in the Selected Coordinate section The Current value and Number of steps text boxes are noneditable The number of steps is calcu lated from the values you provide Once you have defined all the coordinates and their values click Start to start the job or click Write to write out the input file for the job Jaguar 7 0 User Manual 81 Chapter 4 Optimizations and Scans 82 4 4 2 Setting up Input Files for Scans To create an input file for a coo
444. rostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability rj m Vibrational frequencies Use available Hessian Thermochemistry IR Intensities Pressure 1 00 atm Atomic masses Most abundant isotopes zill Start temperature 298 15 K Scaling Increment 10 00 K wv None Number of steps 1 v Pulay SQM method B3LYP 5 31G factors Output units Scaling factor kcal mol w kJ mol User defined Value 0 8992 Job B3LYP 6 31G Single Point Energy Frequencies Start Read Write Edit Reset Close Help Figure 3 9 The Properties tab showing controls for vibrational frequencies 3 11 2 Atomic Masses For frequency calculations the atomic mass used for each element is that of its most abundant isotope by default However you can choose to use an average of the isotopic masses weighted by the abundance of the isotopes by selecting Average isotopic masses from the Atomic masses option menu 92 Keyword massav 0 in the gen section 93 Keyword massav 1 in the gen section Jaguar 7 0 User Manual 59 Chapter 3 Options 60 3 11 3 Scaling of Frequencies Because the errors in quantum mechanical calculations of frequencies are often fairly predict able it is sometimes desirable to scale frequencies by one or more factors Scaling methods can also
445. rovides one contracted function for He the 1s function whose derivative is a p type function the last number entered on that line 2 dictates that a p type function be constructed using the contraction coefficients and exponents that correspond to that derivative function as explained in the previous paragraph 9 3 2 Sample File The following sample daf file lists the dealiasing set for H and He for a 6 31G basis set Blank lines may be added for readability and data may be spread over multiple lines Jaguar 7 0 User Manual Other Jaguar Files Chapter 9 dafv0300 number of rows set neighbors cutoffs distances number of sets atom row 2 neighbors 3 0 5 0 7 0 9 0 BASIS 6 31G H 1102 0 040634 0 080953 0 161278 0 321306 0 640122 1 275283 2 540684 5 061679 10 084136 1 100000 He 2 102 0 071497 0 145957 0 297964 0 608279 1 241774 2 535023 5 175131 10 564786 21 567514 1 100000 247 Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files 248 0 3 3 3 0 0 Q9 P H 0 0 0 0 0 7 00 5 0 0 0 2 1 0 00 7 3 2 5 0 0 0 2 1 0 0 03 02 1 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 00000 0 0 0 0 0 7 0 0 5 0 0 0 2 T 9 0 073 2 5 000 2 L 3 0 03 02 1 0 0 0 2 T 0 00 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 0 0 0 3 7005 0 0 0 2 1 0 03 7 3 2 5 0 0 0 2 1 0 0 03 02 1000 2 1 0 00 0 0 0 0 0 0 0 0 0 0 0 00000000 0 0 0 Q0 3 3 3 0 0 0
446. rrently used gconv5 1 8x107 Maximum element of nuclear displacement gconv6 1 2x107 rms of nuclear displacement elements gconv7 5 0x10 Difference between final energies from previous and current geometry optimization iterations 8 5 11 Geometry Scan Keywords Keywords for defining the initial wave function and the initial Hessian for geometry scans coordinate scans are listed in Table 8 22 These keywords can also be used with IRC scans Table 8 22 Keywords for geometry scans Keyword Value Description scanhess 0 Use the final Hessian from the last geometry step as the initial Hessian for the next step 1 Use the Hessian specified by the inhess setting as the initial Hessian for the next step The Hessian in a hess section is only used for the first step unless inhess is explicitly set to 2 scanguess 0 For geometry scans use converged wave function from previous step as initial guess for current geometry 1 For each step in a geometry scan generate the initial guess wave func tion according to the iguess setting Jaguar 7 0 User Manual 183 Chapter 8 The Jaguar Input File 184 8 5 12 Intrinsic Reaction Coordinate IRC Keywords IRC scans have been implemented in Jaguar using the methods described in Ref 178 The implementation includes IRC and minimum energy path MEP calculations The calculations start at a transition state and move downhill in energy along the reaction path toward a minimum of the potential ene
447. rse 2 Basis functions are sorted into Imedium Ifine lufine lgrad short and long range gname 20 Specifies which parameter set from gcoarse 1 gmedium 2 gfine 3 grid file should be used for grid gufine 4 ggrad 4 glmp2 4 e g 2 for second glmp2grad 2 geldens 4 1 Use spherical charge fitting grid gcharge generated within Jaguar for grid listed by name 2 Use cubic charge fitting grid gener none ated within Jaguar for grid listed by name 3 Use cubic electron density grid gen none erated within Jaguar for grid listed by name 6 Use grid and weights from file spec none ified by GPTSFILE line in input file for grid listed by name dname gt 0 Specifies which dealiasing function dcoarse 1 dmedium 2 dfine 3 from the daf file should be used dufine 4 dgrad 5 8 5 26 Memory Use Keywords Some of the memory use for Jaguar can be controlled through keywords These keywords may be particularly useful if you are experiencing problems running jobs due to memory related failures as described in Section 11 2 on page 288 Memory use keywords are listed in Table 8 39 along with their default values and a descrip tion of their uses If you want to change some memory use but do not have a detailed knowl edge of the code do not change the variable mxpr Finally the iq keywords allow you to choose when to compute the full least squares fitting matrix Q from the smaller matrix S R wR and whether to
448. rticular torsional angle would cause parts of the molecule to crash into each other if the torsional angle s value were suddenly imposed you can instead specify the desired value for the torsion as a dynamic constraint The optimizer changes the torsion gradually during the optimization so that the final torsional angle is as close as possible to the desired torsional angle Defining dynamic constraints is handled in the coord section which is described in Section 8 4 on page 160 You can make a constraint dynamic by editing the input file or by using the controls in the Optimization tab To make a constraint in the Constraints table dynamic select the table row then select Dynamic in the Selected constraint section next to the table and enter the value that you want the constraint to converge on in the Target value text box This value is copied to the Target column of the table and added to the variable definition in the coord section 4 3 Transition State Optimizations To perform transition state searches with Jaguar you can use either a simple quasi Newton method that searches for the transition state nearest to the initial geometry or quadratic synchronous transit QST methods also known as synchronous transit quasi Newton STQN searches We generally recommend using QST methods any time you can provide both reac tant and product geometries To set up a transition state search choose Transition State Search from the Jaguar subm
449. ructure By default the entire input file is available for editing In Structure mode only the geometry is displayed and a Structure menu is added to the menu bar If you are editing geometries for a transition state search or an IRC scan all three geometries can be edited The editing area has tabs for each of these geometries labeled Reactant Product and Transition State The Structure menu provides options for modifying the geometry input The Convert to Z matrix and Convert to Cartesians options switch between Z matrix format and Cartesian format The option Assign Unique Atom Labels converts all atom labels to the form E where El is the standard element symbol Fe for iron for instance and is the atom number in the input list 1 for the first atom 2 for the second and so on This option guarantees that all atoms have unique atom labels which is required by Jaguar Unique atom labels are assigned automatically if Jaguar detects any ambiguity in the labels You can display the atom labels in the Workspace by choosing View Atom Labels The remaining option on the Structure menu is useful for transition state searches but not for other Jaguar jobs This option is described in Section 4 3 on page 74 The changes you make are automatically saved in the Maestro project and are reflected in the panel settings You can view the changes to the geometry in the Workspace by clicking Preview Note Counterpoise atoms constraints and coordi
450. ry and use it as the working directory for input and output Copy the specified files into the directory The default is the job submission directory Specify jaguar run command line options Set options to apply to subsequent jobs Options can be specified over multiple lines by using on the first line and on subsequent lines Options are listed in Table 10 5 Copy the specified files from WORKDIR to OUTDIR at the end of the job The file list can be spread over multiple lines by using on the first line and on subsequent lines If set to _ALL_ then output files from all subjobs are copied if set to _LAST_ only the output files from the last subjob are copied The default is _ALL_ The files that are copied become the output files of the batch job Specify the structure output Maestro file of the batch job This is a file in WORKDIR that is copied to OUTDIR at the end of the job and that will be monitored and incorporated by Maestro Continue to the next job if a job step fails The default is to stop exe cution of the batch script and exit Purge the job record for each job after it finishes Exit from the batch script Jaguar 7 0 User Manual 273 Chapter 10 Running Jobs 274 The syntax for job specifications is as follows template name new name options Each job specification defines a single Jaguar job For each job the following steps are taken 1 The template file template name in is read This
451. ry of the complex Useful if the input geometry for the comples is already accurate noopt torsions Freeze all torsions during optimizations Gradients associated with weak tor sions can be noisy causing the optimizer to wander and take more cycles than necessary for convergence fast Fast mode use extrapolated DFT energies to calculate binding energy instead of LMP2 energies This mode is not quite as accurate as the normal mode where filenames are one or more Jaguar input files or Maestro structure files only one file type not a mixture of both and the options are described in Table 10 7 For each complex a job directory called name hydrogen bond is created in the current working directory where name is the stem of the structure file name and the job files for that complex are written to this directory When the job finishes a file called name hydrogen bond out is written to the current working directory The content of this file should be self explanatory Hydrogen bond energy calculation for h2o h2co in Energy units are kcal mol BSSE corrected cc pVTZ f binding energy 3 98 cc pVTZ f BSSE correction 1 08 BSSE corrected cc pVQZ g binding energy 4 37 cc pVQZ g BSSE correction 0 41 Extrapolated binding energy 4 77 The binding energy calculated with the two basis sets is printed along with the corresponding BSSE corrections As the size of the basis set increases the size of the BSSE
452. s 48 3 8 4 Orbital Treatment Convergence difficulties can be encountered when orbitals of different symmetries swap You can fix the population in each symmetry by selecting Fixed symmetry populations This option is useful when you are running calculations on different occupations of degenerate d orbitals or if you want to converge on a state that is not the ground state but can be distin guished by the occupations of orbitals of different symmetries By default the final wave function is not localized You can localize the valence orbitals after the wave function is computed with either the Boys procedure 61 or the Pipek Mezey procedure 62 by choosing from the Final localization option menu The Boys procedure localizes the doubly occupied orbitals by maximizing the term EjgKolrlo Arie 2 Pipek Mezey localization is performed by maximizing the sum of the squares of the atomic Mulliken populations for each atom and occupied orbital See Section 5 6 on page 125 to find out how to print the localized orbitals resulting from either method Both of the available localization methods scale as N with basis set size However the use of molecular symmetry is turned off for the entire job whenever you perform a final localization so for fastest results you might want to run a job without localization then restart the job after turning on localization in the new input file See Section 6 5 on page 136 for information on restar
453. s Keyword Value Description ipl 2 Gaussian function list for basis set ip3 2 Gaussian function list for dealiasing functions ip4 2 Number of dealiasing functions used ip5 2 Memory disk and i o information ip6 2 Timing information user CPU and user system CPU 2 Timing information user cpu and wall clock ip7 2 Grid shell locations Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 32 Output keywords and their settings Continued Keyword Value Description ip8 2 Gaussian function list for derivatives of basis functions ip11 2 Bond lengths and angles 3 Same as setting ip11 2 but includes all internuclear distances regardless of connectivity and torsions 4 Same as setting ip11 3 but includes all possible angles regardless of atom connectivity 5 Same as setting ip11 4 but includes all possible torsions regardless of atom connectivity ip12 2 Connectivity table ip13 2 Eigenvectors and eigenvalues of overlap matrix ip18 2 Overlap matrix ip19 2 One electron Hamiltonian ip20 2 Additional output from RwR including inverse condition numbers and dealiasing functions associated with small eigenvalues of RwR ip23 2 Additional DFT grid information ip24 2 All keyword settings including internal ones ip25 2 Multipole moments in atomic units and Debye ip26 2 Geometries in bohr as well as Angstroms ip70 2 Extra geometry optimization details ip170 2 Localized orbital locations and LMP2 pair energies for lo
454. s are used for pseudospectral SCF iterations or for charge fitting Table 8 37 Pseudospectral charge fitting and electron density grid types Name Description coarse Least expensive least accurate level medium Used for most SCF iterations fine Sometimes used for a limited number of iterations ufine Ultrafine most accurate level grad Used in gradient computation Imp2 Grid used for LMP2 energy calculations Imp2grad Grid used for LMP2 gradient calculations charge Grid used for charge fitting eldens Used for electron density calculations a These names are used in the grid related keywords described in Table 8 38 The grid related keywords and their allowed and default values are given in Table 8 38 where name corresponds to one of the grid types listed in Table 8 37 As an example gmedium 2 indicates that the medium grid to be used is the second one listed in the grid file while geldens 3 indicates that an electron density calculation should use a cubic grid You can read in your own set of grid points and weights by using the game 6 option and the GPTSFILE line of the input file which is described in Section 8 1 on page 155 Jaguar 7 0 User Manual 211 Chapter 8 The Jaguar Input File 212 Table 8 38 Keywords for specification of length scales for sorting of basis functions grid usage and dealiasing function usage Keyword Value Description Default for Iname 1 Only one length scale used Icoa
455. s automatically The appropriate keywords are listed in Table 8 6 The Lewis dot structure code finds several alternative Lewis dot structures for resonant mole cules assigning bonds as single double or triple bonds unambiguously For instance it finds two structures for benzene depending on the assignment of the pi bonds For these cases you might want to run Jaguar with lewdot 1 and lewstr 0 which will cause it to print out all Lewis dot structures it finds then exit At that point you can figure out which structure you want to use to set the GVB pairs set lewstr igvball and igvbsel accordingly and set lewdot 1 If you know there is only one reasonable Lewis dot structure for the molecule you can set igvball and igvbsel At that point lewdot and lewstr are set to 1 by default The values for igvbsel are easier to remember if you associate the number 1 with sigma pairs 2 with pi pairs and 4 with GVB lone pairs Then to print out any combination of these pair types you set igvbsel to equal the sum of the numbers associated with the pair types you want to print Table 8 6 Keywords for evaluation of Lewis dot structures and application of that information to GVB pair settings Keyword Value Description lewdot 0 Do not find Lewis dot structure s or use them to set GVB pairs 1 Find Lewis dot structure s and continue on with calculation lewdot 1 by default if igvball gt 0 1 Find Lewis dot structure s and exit wi
456. s described in Section 3 10 1 on page 52 The output from ch begins with the moments calculated for the quantum mechanical wave function in the format for multipole moment calculations Next the electrostatic poten tial fitting information is provided as described above Finally the components and totals of the moments recalculated using the electrostatic potential charges are reported 5 3 7 2 Polarizabilities and Hyperpolarizabilities If you calculate polarizabilities and hyperpolarizabilities with the coupled perturbed HF method the tensor elements in au appear in the output from the program cpolar which runs after the SCF calculation Alternatively if you use the finite field method to calculate the polar izability and or first hyperpolarizability of the molecule the output includes data from all the SCF calculations involved See Section 3 10 on page 52 for details on the methods used to calculate polarizability and hyperpolarizability The data from the program scf includes the virial ration NIT Before each SCF calculation used for the polarizability evaluation the program polar runs and outputs the electric field in au used for the SCF calculation whose output appears immediately afterwards When all calculations needed for the finite difference method have been performed the program polar outputs the polarizability tensor in au the first hyperpolarizability tensor in au if it has been calculated and the dipoles from each SCF cal
457. s for each element of interest in the same basis set and with the same method as for the molecule of interest Shieldings are calculated for all atoms including those with ECPs Shielding constants for atoms whose core is represented by an ECP should be treated with caution because the main contributions come from the core tail of the valence orbitals which is largely absent at ECP centers Chemical shifts derived from these shielding constants might display the correct trends but are likely to have the wrong magnitude 3 10 7 Molecular Properties from SM6 Calculations When an SM6 calculation is carried out in Jaguar several additional molecular properties are automatically calculated because they are necessary for the SM6 calculation L wdin Population Analysis L wdin populations 165 166 are computed for each atom in the gas phase and in the solution phase e Redistributed L wdin Population Analysis When basis sets containing diffuse func tions that is 6 31 G or 6 31 G are specified with SM6 redistributed L wdin popu lations 167 are computed for each atom in the gas phase and in the solution phase e Mayer Bond Orders Mayer bond orders 168 170 are computed between each pair of atoms in the gas phase and in the solution phase To print the Mayer bond order matrix you must specify ip378 2 in the gen section e CM4 Partial Atomic Charges CMA partial atomic charges 157 are computed for each atom in the ga
458. s for each orbital The orbital file name stems are of the form jobname_spin_MO_ where spin can be alpha or beta and is the orbital index number For instance the fifth orbital from the job h2o would be written to the file bio alpha MO 5 vis A plt file begins with an echo of the plot section used to generate it The rest of the lines in the p1t file contain values of the relevant property to be plotted on the grid first varying the z coordinate then the y coordinate then the x coordinate the loop over z values is the innermost loop The vis file is a binary file Note The plot section is deprecated but is still generated internally and written to the p1t file You can still include a plot section in an input file 8 6 The gvb Section The gvb section whose GUI equivalent is described in Section 3 6 on page 43 is not keyword based The section should contain the pair settings in any order unless you are using the Lewis dot structure keywords described in Section 8 5 6 on page 165 Each line describing a bond pair should contain three integers which specify the type of bond 1 for sigma 2 for pi 3 fora second pi in a triple bond and the atom number labels of the two atoms in the GVB pair Each line describing a lone pair should contain a number identifying the lone pair followed by the number or atom label of the atom associated with the lone pair and the same atom number or label repeated once more Either all or none of the
459. s of polarizabilities first hyperpolarizabilities B and second hyperpolarizabilities y are Jaguar 7 0 User Manual 187 Chapter 8 The Jaguar Input File 188 2 3 4 d E dE dE uf GF dF Bik TF dF dF qEJF dF dF If you want to calculate polarizabilities with the old definition you must set iopt332 332 in the gen section and you can only calculate and B for closed shell wave functions Table 8 25 Keywords for charge fitting multipole moment and polarizability and hyperpolariz ability calculations Keyword Value Description icfit 0 Do not do electrostatic potential fitting 1 Fit electrostatic potential to atomic centers default for PBF solvation calculations 2 Fit electrostatic potential to atomic centers and bond midpoints cfiterr LIT Allowed error in electrostatic potential charge fitting when fitting is constrained to reproduce multipole moments wispc 0 75 Spacing in bohrs of rectangular grid for electrostatic potential fitting incdip 0 Use only total charge as constraint in electrostatic potential fitting 1 Use charge and dipole moment as constraints in electrostatic potential ESP fitting 11 Use charge dipole moment and quadrupole moment as constraints in electrostatic potential ESP fitting 111 se charge dipole moment quadrupole moment and octupole moment as constraints in electrostatic potential ESP fitting ijk Compute ESP fitted charges using total charge
460. s phase and in the solution phase according to gr E gh gt Dy m Ck mBk m Bk m met 89 Keyword nmr 1 in the gen section Jaguar 7 0 User Manual 57 Chapter 3 Options 58 where the summation goes over atoms m in the molecule q is the partial atomic charge from either a L wdin population analysis nondiffuse basis sets or a redistributed L w din population analysis diffuse basis sets B is the Mayer bond order between k and m and C and D are empirical parameters that depend on the basis set and on the atomic number of k and m Currently CM4 parameter sets are only available for the basis sets used by SM6 3 11 Frequencies and Related Properties By selecting Vibrational frequencies in the Properties tab you can request calculations of frequencies infrared ir intensities and thermochemical properties heat capacity entropy enthalpy and Gibbs free energy The results of frequency calculations can be animated in Maestro 3 11 1 Frequencies Vibrational frequency calculations are available for HF GVB LMP2 and DFT wave functions in gas phase or in solution but are not available for GVB LMP2 calculations Numerical frequencies cannot be computed for unrestricted HF or DFT wave functions For gas phase HF and DFT jobs with basis sets that allow pseudospectral calculations and do not include f functions Jaguar computes analytic frequencies See Section 3 2 on page 30 for more information on basi
461. s sets Otherwise Jaguar uses energies obtained at perturbed geome tries to calculate the numerical derivatives of the analytically computed forces Analytic frequency calculations are much faster than numerical frequency calculations However when frequencies are calculated analytically molecular symmetry is turned off for the job Therefore if you want to compute analytic frequencies for large highly symmetric molecules you should first run any other computationally intensive portions of the job such as geometry optimization then use the restart file as input for an analytic frequency job See Section 6 5 on page 136 for information on generating restart files and restarting jobs If you want to calculate frequencies numerically instead make the keyword setting nmder 2 in the gen section of the input file as described in Section 8 5 on page 163 To compute frequencies and any frequency related properties from the Hessian available at the end of a job either an initial Hessian if it was never updated or the updated Hessian select Use available Hessian 90 Keyword ifreq 1 in the gen section 9 Keyword ifreq 1 in the gen section Jaguar 7 0 User Manual Chapter 3 Options Jaguar jaguar DE Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Properties select to edit options L Surfaces MO density potential Atomic elect
462. s to produce a different number of negative Hessian eigenvalues for a non stationary point If you select the mode to follow based on the results of a vibrational frequency calculation you might discover that the mode actually followed is different and that the number of negative Hessian eigenvalues has changed There are two ways around this problem The preferred way is to use the QST guided algorithm which automatically selects the mode that best connects the reactant and product geometries with the transition state guess geometry In this case there is no need to select an eigenvector or to set the itrvec keyword If you do not wish to use the QST method then you should check the output file from your transition state search job while it is running to ensure that the desired mode was selected For each negative Hessian eigenvalue Jaguar prints out the internal coordinates that dominate the corresponding eigenvector If you find that the wrong mode is being followed kill the job and select the desired eigenvector index either in the GUI or by setting itrvec in the gen section of the input file The order and the character of the eigenvectors can change during an optimization To ensure that the optimization follows the eigenvector that most closely correlates with the one chosen in the previous iteration select Follow same eigenvector Otherwise the optimization follows the eigenvector of the same index number as the previous iteration
463. scribes the internal coordinates and optimization variables as stretches bends or torsions and indi cates how it generates a new geometry by altering the relevant coordinate by the amount described by the step size The new geometry generated for Hessian refinement is used to obtain energy and gradient information a process that requires the programs onee grid and rwr to run and generate Jaguar 7 0 User Manual Chapter 5 Output output in the usual formats This is followed by output from the program scf which now starts with the calculation type and the table showing the energy output from each SCF iteration skipping the listed information about electrons orbitals and so on The output continues with output in the usual formats from der1a rwr and der1b The information obtained on that geometry is then used in geopt which runs a second time reporting similar information about the planned changes to the molecular structure for the next Hessian refinement step if there is one and reporting the change in total energy from the original geometry to the geometry for the first Hessian refinement step as well This process of altering single coordinates from the original geometry and calculating energies and gradients for the changed geometry continues until all requested Hessian refinement steps have been performed which the output indicates with a line beginning Hessian optimization completed At that point geopt performs a ge
464. scripts counterpoise py and hydrogen bond py These scripts are described in the sections below 10 2 4 1 counterpoise py The script counterpoise py can be used to calculate a counterpoise corrected binding energy of a complex consisting of two non covalently bound molecules You can run this script from the command line using the following syntax jaguar batch counterpoise filename where filename can be either a Jaguar input file or a Maestro structure file A job directory called filename counterpoise is created in the current working directory and the job files for all calculations are written to this directory When the job finishes a file named file Jaguar 7 0 User Manual 279 Chapter 10 Running Jobs 280 name_counterpoise out is written to the current working directory This file contains the counterpoise corrected binding energy and the counterpoise correction energy If the basis set and level of theory are not specified in the input file then each job runs using the same default settings as for Jaguar jobs launched from Maestro the default level of theory is DFT with the B3LYP functional the default basis set is 6 31G and no geometry optimi zation is performed You can specify keyword settings in the input file if it is a Jaguar input file but you can also specify settings on the command line For example if you want to optimize the geometries of the fragments and of the complex using the X3LYP functional t
465. ser for selecting a Jaguar input file to read in See Section 2 5 on page 17 Write Opens a file browser for writing the current geometry and settings in the Jaguar panel as an input file or for writing the current settings as a batch script Edit Opens the Edit Job dialog box in which you can edit the contents of the input file Any changes you make in this dialog box are reflected in the settings in the Jaguar panel You can also add keywords that are not available as GUI settings see the next section Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro Edit Job DEEN File Edit Structure Help Edit v Inputfile Structure C1 33 9573083333333 33 1980866666667 17 0409950000000 A c2 33 2550083333333 34 4144866666667 17 0409950000000 c3 31 8505083333333 34 4144866666667 17 0409950000000 C4 31 1483083333333 33 1980866666667 17 0409950000000 CR 31 8505083333333 31 9816866666667 17 0409950000000 C6 33 2551083333333 31 9816866666667 17 0409950000000 H7 35 0607083333333 33 1980866666667 17 0409950000000 H8 33 8068083333333 35 3700866666667 17 0409950000000 H9 31 2988083333333 35 3700866666667 17 0409950000000 H10 30 0449083333333 33 1980866666667 17 0409950000000 H11 31 2988083333333 31 0261866666667 17 0409950000000 H12 33 8068083333333 31 0260866666667 17 0409950000000 P OK Cancel Preview Help Figure 2 2 The Edit Job dialog box with Structure selected
466. sess 134 227 choosing ffe 131 132 file information for 237 242 243 GVB from HF wave function 198 tele 133 134 information in output eee 93 input file section for 229 230 KEY doi 198 orbital output in format for 126 209 output of GVB senarrei 208 printing orbitals after 125 208 restarted calculations eeseeeeeeeeeeeeeeee 132 stopping after 139 198 transition metal systems 131 132 133 134 input file 155 158 defining fragments esses 227 156 158 251225 233 description of sections echoing in output file editing ione cte een bags 237 e aia tease coe niea 140 general description and format 155 158 in jaguar run command 266 268 keywords eet nns 163 213 ntur 266 reading in Maestro 17 18 li 136 137 uc FRERES 21 section delineators sess 156 selecting in Maestro 25 spacing characterg 156 summary of Sections ssssesiseeerererereeee 157 input file sections atomic 219 227 connect 160 163 coord 160 163 un 233 fields inen eed 231 gen 163 213 guess 220 230 gvb 217 218 ham s 231 232 Eegenen EE 228 229 ee 168 218 MVD tS 23 Ia
467. set Close Help Figure 5 1 The Output tab Jaguar 7 0 User Manual 121 Chapter 5 Output 122 Echo input file and parameter list If you turn this output option on the output from the program pre includes an echo of the input file a description of the path which indicates the Jaguar programs run and a list of keyword settings including those made by default and program parameters This option is likely to be useful primarily for people who have a detailed knowledge of the code itself Memory disk and i o information The memory information provided by this option is given for most of the routines used during the run under the heading dynamic memory statistics Current and maximum values for the number of arrays their size in 8 byte words and their size in bytes as well as the type of vari ables used e g real 8 are listed The total and index i o for the J and K matrices in Mwords are also provided after the energy output from the SCF iterations Detailed timing information If you select this option the CPU time in seconds spent in various Jaguar programs is listed in the output Geometries in atomic units also This option allows you to print the geometry output in atomic units as well as in the default units angstroms Multipole moments in atomic units also If you choose to calculate multipole moments by making the appropriate setting in the Proper ties tab this option al
468. set automatically depending on the basis set as described in Section 3 2 Possible settings for numd are shown in Table 8 27 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 27 Keyword to determine the number of d functions Keyword Value Description numd 5 Use 5 d functions regardless of basis set 6 Use 6 d functions regardless of basis set 8 5 17 Keywords for SCF Methods Many of the keywords that control the SCF calculation can be set from the SCF tab as described in Section 3 8 on page 45 The other keyword settings corresponding to SCF tab settings are described in Section 8 5 19 The SCF keywords are described in Table 8 28 The keyword settings for convergence are somewhat complicated and the defaults vary depending on the settings of other keywords The keywords for convergence thresholds are econv the energy convergence criterion which is the maximum difference in energy between one SCF iteration and the next required for convergence and dconv the criterion for the root mean square change in density matrix elements The default value of econv is normally 5 0x10 hartrees However for polarizability or hyperpolarizability calculations econv is 1 0x10 hartrees by default When the root mean squared change in density matrix elements for a polarizability hyperpolarizability or geometry optimization calculation is less than dconv whose default value is 5 0x10 5 the calculation is considered to
469. sible states in turn to locate the true ground state You can select states by setting the istate keyword in the gen section to the index of the state listed in the output from hfig An example of this output is given in Section 5 2 on page 92 If you want to examine the coefficients of the MOs to see which state is which set ip105 7 6 2 SCF Convergence Generally Hartree Fock wave functions for simple organic molecules converge in fewer than 10 iterations while complex calculations involving higher level methods or open shells may take a few extra iterations Molecules which include transition metals generally converge more slowly however Make sure your job has really converged and did not simply end because it reached the maximum number of SCF iterations a number set in the SCF tab If a job gives poor SCF convergence you can try either modifying the convergence methods used or improving the initial guess To modify the convergence methods try any or all of the following settings Change the Accuracy level setting in the SCF tab to Ultrafine This corresponds to the key word setting iacc 1 which causes the job to use denser pseudospectral grids and tighter cutoffs and generally increases computational costs by a factor of two to three Note however that as of Jaguar v7 0 this action is no longer necessarily because if Jaguar detects that the SCF is not converging it automatically sets iacc 1 Select GVB DIIS from the Convergence
470. sified as acids and bases for bases it is the pK of the conjugate acid that is computed Unless otherwise noted the values are for aqueous solution The largest set of test cases examined have been for carboxylic acids and nitrogen bases in heterocyclic rings The latter cases have minimal conformational flexibility and hence should be easier to handle and this is indeed reflected in the remarkably low average error of 0 2 and maximum error of 0 4 that we observe The carboxylic acids include some examples with polyfunctional groups and significant flexi bility We have not carried out an exhaustive analysis of the conformational energetics for these cases hence much of the deviation from experiment that we report may be due to this Never theless the errors are quite respectable Jaguar 7 0 User Manual 309 Chapter 13 The pK Prediction Module The largest overall error is that for alcohols This is to be expected because the experimental values themselves are subject to greater uncertainty Most of the pK values are higher than 14 so the leveling effect of hydroxide makes the determination of the aqueous pK difficult Table 13 1 Functional groups for which pKa parameters are available Maximum RMS Absolute Functional Group Deviation Deviation ACIDS alcohol 1 0 2 5 phenol 0 2 0 3 carboxylic acid 0 6 1 5 carboxylic acid conjugated 0 5 0 9 thiol 0 4 0 6 thiophenol 0 2 0 6 o nitrophenol 0 6 1 4 sulfonamide 0 7 1 5 hydroxa
471. sis file and the second gives the number of electrons for that atom included in an effective core 0 for the basis sets whose names do not start with LA The line after that lists the orbital number 1 if it is the first orbital listed for that atom 2 if it is the second and so on the orbital occupation i e the number of electron pairs in that orbital and the orbital energy in Hartrees That orbital s coefficients for each basis function for the given atom and basis set s follow on the next line s When all of the orbitals for that atom have been specified a line with 4 characters indicates the end of the information for that atom and the data for the other atoms is listed Similar information for each other basis set follows If you want to set up your own atomig file you can do so if you use the format described above To use the file in a Jaguar calculation you must add a line saying ATOMIGFILE filename to the input file for the job You can specify a file on another host or under another account name on that host by listing the file name in the format host filename or user host filename 9 3 The Dealiasing Function File When Jaguar fits a function s grid point values to a basis set to find the applicable basis set coefficients for the function it uses dealiasing functions to reduce errors The dealiasing func tions span the function space determined by the grid more completely than the basis functions s
472. ss You might want to try this option if you encounter convergence difficulties The third possibility for the GVB initial guess is to read in a GVB wave function from the input file s guess section and to use that as the initial guess for the calculation Keyword isymm 8 in the gen section Keyword ihfgvb 2 in the gen section or keyword ihfgvb 0 if iguess is not 1 Keyword ihfgvb 1 in the gen section Keywords ihfgvb 0 and iguess 1 in the gen section Dg mum Jaguar 7 0 User Manual Chapter 6 Using Jaguar 6 1 3 Initial Guess for Molecules Containing Transition Metals For transition metal containing systems particularly organometallics you can often obtain superior results by improving the initial guess wave function Jaguar automatically generates high quality initial guesses for transition metal containing compounds if you supply the program with information about the charges and spins of the fragments in the compounds it uses that information when generating the guess Here a fragment is defined as either a collec tion of one or more transition metals that are bonded together or one or more non transition metal atoms bonded together Put another way each fragment is simply a group of atoms that would be bonded together even if all bonds between transition metal atoms and non transition metal atoms were broken Typically the system is broken into ligand fragments and transition metal fragments or adso
473. ss but are in the converged wave function To use thermal smearing choose a method from the Thermal smearing option menu and enter a value in the Initial temperature text box More information on this method can be found on page 197 Finally you can attempt to force convergence by selecting the Force convergence option This option starts with a large level shift and adjusts the value during the calculation and runs at ultrafine accuracy level Use this option with caution To speed up convergence Jaguar uses one of a number of convergence acceleration schemes which are available from the Convergence scheme option menu We recommend using the default Direct Inversion in the Iterative Subspace DIIS or GVB DIIS SCF convergence schemes 11 125 whenever possible The DIIS method generally performs better but for jobs with SCF convergence problems GVB DIIS may give improved convergence The DIIS method can be used with any wave function including those with multiple open shells and multiple GVB pairs You can also use the OCBSE convergence scheme 22 although it is generally much slower than DIIS 57 Keyword vshift in the gen section 58 Keyword ifdtherm in the gen section 59 Keyword fdtemp in the gen section 60 Keyword iacscf 1 in the gen section 61 Keyword iconv 1 in the gen section 62 Keyword iconv 4 in the gen section 63 Keyword iconv 3 in the gen section Jaguar 7 0 User Manual 47 Chapter 3 Option
474. store it on disk Names and default values in bold italics for these keywords are indicated in Table 8 40 If a grid is used only once per calculation as the fine ultrafine and gradient grids generally are setting its iqname value to 0 saves disk space and costs no CPU time Setting the iqname values for other grids to 0 adds some CPU cost but saves some disk space Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 39 Keywords related to memory and disk use Keyword Default Description idynmem 256 Dynamic memory in MB to be allocated for LMP2 calculations Suggested optimum value is machine memory 256 mxstrip 200 Information for matrix elements evaluated on basis functions stored in core in strips of mxstrip N words rather than N words at a time where N is the number of basis functions mxpage 1000 For pseudospectral evaluation of J and K on grid points in pro gram scf memory is allocated ngblok mxpage words at a time as needed where ngblok is a parameter currently set to 128 nbuck 64 Grid blocks are split up into subblocks whose points are all on the same atom and in the same region of space with at most nbuck points where nbuck lt ngblok ngblok is the maximum number of grid points per grid block currently set to 128 nbcmax 1000000 Maximum memory in words used by overlap and kinetic energy integral package excluding final matrices themselves ndisk 5000 Atomic strips of
475. stro working Output scratch working displacement convergence criteria based on 69 keywords for convergence criteria 183 display host see 283 285 286 Display Options dialog box 66 dsoly program uieitesieeteticeenitis 234 dummy atoms in charge fitting esses 110 in the Hessiali eite 228 in Z matrix p ti 13 dynamic constraints eee 74 161 E Edit Job dialog box 8 effective core potentials ECPs basis Sets fot ceterae 33 35 in atomic guess file sssss 243 in basis set file hes 239 241 NMR shielding constants AT eigenvector following in transition state optimizations keywords eee ette 179 180 Option TE 78 use of Hessian refinement 79 ee EE 234 Jaguar 7 0 User Manual 335 Index 336 electric field for polarizability calculations input file section ite eine 231 KEY word e erre 189 SEMINE seios 56 electron density keywords nre 189 211 output from calculation 113 apre mE 63 electron density output file 113 189 electrostatic potential in resp file soient 207 output on a grid 190 Le m 63 electrostatic potential fitting 52 54 c
476. sts are on separate local area networks To handle these distinct sites you must use a personal schrodinger hosts file Each host line in the file should include your user name on that host in the following format host sgi username calculation hostname where the name of the machine in the host field matches that in the uname n command output for that machine username is replaced by your user name and calculation hostname is replaced by the name of your execution host See the Section 2 1 of the Job Control Guide for details on how to construct your own schrodinger hosts file 11 2 Other Problems Some other problems you may encounter are detailed below along with solutions or explana tions You cannot read in a particular file as input Make sure you are choosing a file of the right file type Also make sure the file name and not just its directory is really showing up in the Selection text box before you click OK The molecular structure for the calculation is not what you expected it to be If you read in a Jaguar input file the geometry is obtained from that file unless you edit the geometry after reading the file Any geometry you entered before reading the file is erased Also if you symmetrize the geometry or set symmetry on for the calculation as described in Section 2 7 2 on page 19 Jaguar may make small changes to the molecular geometry If these changes are a problem you should avoid symmetrizing the geometry an
477. such matching description exists in the Lewis file the atom is assigned the default radius for that element Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files Atom type descriptions in the Lewis file should be preceded by a heading beginning RADII TYPE 01 for information applying to HF GVB or DFT wave functions or RADII TYPE 02 for information for LMP2 wave functions After that each atom type description is listed Blank lines are allowed in an atom type description list and as long as some spacing exists between numbers and comments on each line the number of spacing characters is irrelevant However keep in mind that the order of the atom type descriptions is important since the first matching description will always be used Each line describing an atom type has six integers one real number and an optional comment in that order The integers describe the atom type while the real number sets the radius in angstroms for that atom type The six integers describe the following characteristics in turn Atomic number for instance 6 for carbon Hybridization of the atom itself e Bonding type of the atom elements it is bound to and order of those bonds Hybridization type of the atom hybridization and elements of atoms to which it is bound Size of ring if any the atom is in Aromaticity of that ring according to Huckel Rule aromatic rings have 4n 2 pi elec trons where n is a non negative integer
478. suffix xyz The file contains all geometries generated during the course of the job except that for solvated geom etry optimizations the file only contains the solvated structures 5 6 Output Options for Orbitals Orbital information can be printed to the output file as well Several possible choices are avail able in the Orbital Coefficients section of the Output tab If you choose to print out orbital infor mation the output from the program pre lists the non default options chosen above the molecular geometry output from pre and indicates the keywords referred to in footnotes throughout this section You can select options that determine the point at which orbitals are printed out from the Calculation Stage list To select multiple items you can use the SHIFT and CTRL keys in combination with clicks The available items are e At end of job Print the orbitals at the end of the job e After HF initial guess Print orbitals used for the HF initial guess e After SCF Print orbitals in atomic orbital space after the SCF converges After final localization Print orbitals after the localization procedure if Boys or Pipek Mezey localization of the wave function has been requested Each iteration in CO space Print orbitals after each SCF iteration in canonical orbital space Canonical orbital eigenvectors with very small eigenvalues are removed from the calculation before the SCF process The number of orb
479. sulting wave func tion otherwise it is generated from the appropriate Jaguar initial guess routine When Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 33 Effect of setting output keywords for files to 2 Keyword Description of What Is Printed When ipi 2 ip90 Molden orbitals file mo1 file ip160 GAUSSIAN 92 input file gau file see text for ip160 3 4 or 5 ip163 GAUSSIAN 92 basis set gbs file ip164 MOM basis set bas file ip165 SPARTAN 4 0 archive file appears in temp directory as spart arc to write arc file to local job directory instead use ip165 3 ip168 GAMESS input file gamess file ip172 RESP Restrained Electrostatic Potential 149 file resp file Set to 3 to include grid weights ip175 XMol file xyz file with geometries generated during optimization ip177 AIMPAC wfn file which works with RHF ROHF but not UHF a Seetext in this subsection for information on ip151 and on other options for ip160 ip160 5 the basis set is included explicitly in the gau file rather than just the basis set name When ip160 4 the trial wave function and the basis set are included The format of the resp file created with the ip172 keyword is as follows The first line contains the number of atoms and the number of grid points at which the electrostatic potential was evaluated The cartesian coordinates of the atoms in bohrs are given next one atom per line Each subsequent
480. t keywords 204 GAUSSIAN input file gau keyword for generation of 140 207 option for generation of 124 139 140 generalized gradient approximation 153 Generalized Valence Bond method see GVB calculations geometry Input 9 16 Cartesian format 10 11 158 formation iens 158 163 input file sections 158 163 keywords neenon 163 output file echoed mm 92 sample calculation esses 4 symmetrizing eee 19 20 troubleshooting eee 288 units keyword for 158 164 230 Z matrix format 11 14 158 160 geometry optimization eene 67 74 calculating forces only 177 constraining bond lengths or angles 14 70 72 160 constraining Cartesian coordinates 11 71 72 convergence criteria 68 69 101 102 182 coordinate system detailed output option for frozen bond lengths or angles for 14 70 72 160 frozen Cartesian coordinates for 11 71 72 GDIIS 1nethod ueri Gere 179 generating input with new geometry 135 in solution esses 51 178 186 initial Hessian for 16 69 70 159 180 228 229 input file section for Hessian 228 229 keywords trente 177 182 limiting step size for 181 182 186 maximum number o
481. t which gives the atom label and coordinates for each atom If the atom labels provided in the geometry are not unique for instance if two hydrogens are each called h this information is preceded by a list of original atom labels and new atom labels assigned by the program The molecule s symmetry is analyzed a process which may involve translating and rotating the molecule These procedures are noted in the output file along with the point group used for the calculation the nuclear repulsion energy and the symmetrized geometry which is used for the rest of the calculation Jaguar 7 0 User Manual Chapter 5 Output One electron integrals are calculated by the onee program which prints the smallest eigen value of the overlap matrix S and the number of canonical orbitals used for the calculation Canonical orbital eigenvectors with very small eigenvalues less than 5 0 x 10 are removed and thus are not counted The eigenvalue cutoff can be controlled by setting the keyword cut20 to the desired value in the gen section of the input file The number of canonical orbitals can also be controlled by setting the keyword ncanorb in the gen section of the input file The program hfig constructs a starting wave function initial guess for a Hartree Fock calcu lation The output from the program hf ig for a default calculation begins with the line initial wave function generated automatically from atomic wave functions Next
482. t Table the entry name appears in the Name text box The names of the input output and log files for your job depend on this name the Jaguar input file is named jobname in the output file is named jobname out and the log file is named jobname 10g For instance if the job name is h2o the results are stored in a file called h20 out within the local job directory If the structure is a scratch entry a default name is selected The execution host the machine that the job will run on can be selected from the Host option menu This menu lists all the hosts available in the schrodinger hosts file The default execution host is localhost which means the machine on which Maestro is running The host name is followed by the number of available processors in parentheses If the host you choose has multiple processors you can run Jaguar in parallel on that host You can enter the number of processors to use in the CPUs text box The default is one processor Jaguar 7 0 User Manual 23 Chapter 2 Running Jaguar From Maestro 24 Note You can distribute batch jobs over multiple processors only if you are using the default batch script or the current settings for the batch script The exception is pK jobs which can be run on two processors because they consist of two independent jobs You cannot run MPI parallel jobs as batch jobs The Scratch directory option menu displays a list of directories on the execution host that can be
483. t files and restarting jobs 3 9 Solvation Settings Jaguar can treat solvated molecular systems with a self consistent reaction field method using either a standard Poisson Boltzmann solver 15 156 9 or the solvation model 6 SM6 approach 157 9 These two models are treated in the next two subsections 3 9 1 Poisson Boltzmann Solvation Model With the standard Poisson Boltzmann solver you can compute solvation free energies and minimum energy solvated structures or solvated transition states The solvation free energy from a geometry optimization is computed as the difference between the energy of the opti mized gas phase structure and the energy of the optimized solvated structure TERENCE RAUL Polen CONSE Conon Aeren e er 1 10 Roce Dor 64 Keyword ipopsym 1 in the gen section 65 Keyword locpostv 0 in the gen section 66 Keyword locpostv 1 in the gen section 67 Keyword locpostv 2 in the gen section 68 Keyword isolv 2 in the gen section 69 Keyword isolv 5 in the gen section Jaguar 7 0 User Manual Chapter 3 Options Jaguar jaguar DIE Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Solvent Water Solvent Model PBF Dielectric constant 80 370 Molecular weight 18 02 g mol Density 0 99823 g mL Probe radius 1 40 A Gas phase reference energy Optimized gas phase structure v Input structure wv V
484. t if the molecular orbitals are transformed so that they are localized on bonds or electron pairs correlation among the occupied pairs can be described by the local orbital pairs and their respective local pair virtual spaces defined from the atomic orbitals on the relevant atom or pair of atoms The localized orbitals can be gener ated by any unitary transformation of the canonical orbitals For LMP2 we use Boys localized 61 orbitals for which the term Ygolro o Irie A is maximized The local virtual space for each atom is defined by orthogonalizing its atomic basis functions against the local ized molecular orbitals The correlating orbitals included in the local virtual space are thus mostly near the atom itself but because of the orthogonalization procedure they are not partic ularly well localized The Jaguar LMP2 program uses Pulay s method 58 59 60 to expand the first order wave function correction VW as a linear combination of determinants formed by exciting electrons from localized orbitals i and j to local virtual space correlation orbitals p and q Jaguar 7 0 User Manual Chapter 7 Theory y 2 y DW werd 18 i2j pq For local MP2 we must iteratively solve the following equation which has been derived in detail by Pulay and Sebo for the coefficients C T T Ky FC S SC F 19 SEI Ful Foto k Here F is the Fock matrix S is the overlap matrix and T is the residual matrix defined by this equation Th
485. t if you restart a run you may not get exactly the same results as you would if you had simply performed a longer run in the first place even if the calculation type is the same The methods used in Jaguar sometimes use data from previous iterations if this information is available but the data may not be stored in the new input file For example the DIIS conver gence scheme uses Fock matrices from all previous iterations for the run and Fock matrices are not stored in new input files However calculations should ultimately converge to the same answer within a standard margin of error whether they are restarted or not If your run aborted or was killed before completion and you want to restart the calculation or start another calculation where that one left off you can look for a file called restart in The file is located in a subdirectory whose name is the same as the job s and which is found within the temp directory for the job which was listed in the Start panel By default the restart in file is written out at the end of the Jaguar programs for calculating the initial guess performing the SCF iterations and calculating a new geometry for geometry optimizations as well as at the end of each SCF iteration To turn off restart in file genera tion the input file output keywords ip151 and or ip152 in the gen section should be set to 0 The restart in file is overwritten each time so that the final version is written either at the e
486. t include effective core potentials Basis Set STO 3G 3 21G 4 21G 6 21G 4 31G 6 31G 6 311G 6 311G 3df 3pd 6 31G tm m6 31G tm D95V D95 MSV cc pVDZ cc pVDZ d without d functions cc pVTZ Atoms Included H Xe H Xe H Ne H Ar H Ne H Ar H Ar H Ar H Zn K Zn H Li Ne H Li Ne Al Cl H Ru Pd Xe H He B Ne Al Ar H He B Ne Al Ar H Ar Ca Ga Kr Jaguar 7 0 User Manual Options Na Xe Na Ar Li Ar H Ar LEE I x kk x kk o op LE WIEN Wo eR tt for H Ar TR kk Method analytic H Ar pseudospectral analytic with or K Xe analytic analytic analytic analytic pseudospectral H Li C F Na Si Cl pseudo spectral others analytic analytic H Ar pseudospectral K Zn ana lytic analytic analytic H Li C F Si Cl pseudospectral others analytic analytic H C F Si Cl pseudospectral others analytic analytic H C F Si Cl pseudospectral others analytic analytic H C F Si Cl Br pseudospectral others analytic of d fns nn O GO CO Refs 77 81 82 84 85 82 84 86 91 87 92 94 97 94 97 87 93 98 99 99 100 101 104 101 104 101 104 Chapter 3 Options Table 3 1 Available basis sets that do not include effective core potentials Continued Atoms of Basis Set Included Options Method dfns Refs c
487. t text box or click Browse and choose a script in the Select Batch Script panel This panel is a file selector with the usual file browsing tools By default information is displayed in the lists and the filter for the current working directory To select one of the supplied Jaguar scripts click Jaguar Scripts in the Directory section then select the script When you select a script the Notes text area shows comments from the batch script When you have chosen the directory choose a script from the list of scripts then click OK The built in scripts are described briefly in Table 2 1 The input files that you select can be pre existing input files or files created from the current structure in the Workspace or from Project Table entries These choices are available from the Source of structures option menu in the Run Batch File panel If you choose Workspace or Selected entries the structures are written to a single Maestro file and the Jaguar input files are created later by the batch facility To select pre existing files choose Selected structure files from the Source of structures option menu then enter a comma separated list of file names in the Files text box or click Browse The Browse button opens a standard file selector labeled Select Batch Inputs with the current directory and its files listed You can select either Jaguar input files or Maestro files for input If you select Maestro files Jaguar input files are constructed la
488. tch directory creation and cleanup and ensures that each job has a unique scratch directory Output files are copied to the working directory while the job is running Detailed information on Job Control can be found in the Job Control Guide Some of this information is repeated here If you intend to run jobs on various hosts you must provide information on the hosts to the job control facility through a file named schrodinger hosts How to provide this information is described in Section 2 1 of the Job Control Guide In addition to using the job control facility you can use the jaguar command to perform a number of job submission tasks The jaguar command is described in the following section and creating batch scripts to submit multiple Jaguar jobs is described in the subsequent section 10 1 The jaguar Command You can use the jaguar command to perform the following tasks among others e Runa job on any machine at your site with any installed version of Jaguar Kill a Jaguar job that you started on any machine at your site Listthe machines on which Jaguar is installed List the jobs that are running on a particular machine If Jaguar is installed on more than one machine at your site you can use the jaguar command on one machine to run kill or list Jaguar jobs on another machine even if you are not logged in to the second machine This section describes in some detail how and when to use the jaguar command The syntax of th
489. ter To select multiple files use SHIFT to select a range of items and CTRL to select or deselect a single item without affecting other items When you have made a selection click OK The input files are passed to the batch script in the order in which they appear in the list To process input files in a particular order you must name them so that they appear in the correct order in the list Jaguar 7 0 User Manual 25 26 Chapter 2 Running Jaguar From Maestro Table 2 1 Description of built in batch scripts Script Description JOBS bat geopt DFT I bat geopt DFT II bat geopt DFT III bat j2 bat pka bat counterpoise py hydrogen bond py _ Select Batch Script ENE Run a sequence of jobs specified by the input files Preoptimize a geometry at the BLYP 6 31G level then optimize at the BLYP 6 31G level Do geometry preoptimizations at the HF 6 31G and BLYP 6 31G level then optimize at the B3LYP cc pVTZ f level Do geometry preoptimizations at the HF 6 31G BLYP 6 31G and B3LYP 6 31G level then optimize at the B3LYP cc pVTZ f level Run a J2 theory calculation 27 Run a pKa calculation See Chapter 13 for details Run a counterpoise calculation See Section 2 4 7 and Section 10 2 4 Calculate binding energy of two molecules that are hydrogen bonded See Section 2 13 and Section 10 2 4 Filter Directories Files JOBS bat LA counterpoise py Yjagquar v70018
490. ter 9 Other Jaguar Files D 243 36058460 3 00000000 41 57647590 36 28476260 13 26491670 72 93048800 3 67971650 23 84011510 0 97642090 6 01238610 1257 26506820 5 00000000 189 62488100 117 44956830 54 52477590 423 39867040 13 74499550 109 32472970 3 68135790 31 37016560 0 94611060 7 12418130 a HAHAHAH em MO PN PN D ON el KKK 9 1 3 Customizing Basis Sets If you want to set up your own basis file you can do so if you use the format described above Generally you must also create an altered version of the atomig file which is described in Section 9 2 although if you are just adding polarization functions to the basis set and these functions are identified by the polarization diffuse function parameter described earlier in this section you can continue to use the usual atomig file Make sure your new basis file contains the 6 31G basis set because the initial guess program needs this basis set If you alter the basis functions in the default basis file only slightly you can use the same names for the basis sets If you change them a great deal you should use a new name so that Jaguar will not attempt to use grids or dealiasing functions that do not match the new basis set If you change a basis set name to something Jaguar does not recognize runs using that basis set will use all analytic methods see Section 3 8 1 on page 45 or the information on the input file gen section keyword nops in Section 8 5 17 on page 193
491. ter all manipu lations have been specified the word end should be included For UHF wave functions the syntax is modified slightly and the alpha and beta spin orbitals are designated by hfiglcmoa and hfiglcmob amp orbman hfiglcmoa i j k 1 p end hfiglcmob pq y r s 0 end amp Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File 8 15 The echo Section The echo section contains only its own label and requests a copy of the input file to be printed in the output file amp echo amp 8 16 The path Section The path section allows you to specify the execution path which determines the order of the Jaguar or other programs to be run If no path section exists Jaguar will use the default path resulting from the settings in other sections of the input file The items listed in a path can be either Jaguar programs UNIX commands or other programs accessible from the executable directory If a program or command is not accessible from the executable directory you must specify the full path for that program with a character at the beginning of the path Table 8 48 gives a brief description of each Jaguar program Table 8 48 Individual programs included in Jaguar Program Description jexec Driver program for all Jaguar executables note inclusion of jexec in path will cause recursive Jaguar calculations pre Reads and checks input including path if any performs symmetry analysis and
492. that could be used for generating surfaces When the job is run each type of output requested is written to a file whose name depends on jobname the name for the job for example h20 and the type of information being plotted Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 41 Keywords for generating plot data Keyword Value Meaning iplotden 0 Do not generate electron density data 1 Generate electron density data iplotspn 0 Do not generate electron spin density data 1 Generate electron spin density data iplotesp 0 Do not generate electrostatic potential data 1 Generate electrostatic potential data iorbla 3 Generate electrostatic potential data 2 Generate electron density data 1 Generate data for all alpha orbitals 0 Do not generate any alpha orbital data 20 Index of first alpha orbital for which to generate data homotn Index of first alpha orbital for which to generate data relative to highest occupied molecular orbital HOMO n can be any positive integer umotn Index of first alpha orbital for which to generate data relative to lowest unoccupied molecular orbital LUMO n can be any positive integer iorb2a 20 Index of last alpha orbital for which to generate data Ignored unless iorb1a is positive homotn Index of last alpha orbital for which to generate data relative to highest occupied molecular orbital HOMO Ignored unless iorb1a is positive n can be any positive integer
493. the input and the new input is written to the file h2o_dft in The same effect is achieved with the job specification SJOB SJOB dft dftname b3lyp and running jaguar batch with the job name h2o as an argument If no options are specified the Jaguar job is run using the template file as input For example if you had a set of input files jobnamel in jobname2 in jobname3 in you could use the following batch input file to run Jaguar for each input file in order Jaguar 7 0 User Manual Chapter 10 Running Jobs jobnamel jobname2 jobname3 Options for each Jaguar job can be set in preceding OPTIONS directives or by an options list appearing in the job specification An options list appearing in the job specification applies only to that job Options specified in an OPTIONS directive apply to all subsequent jobs unless superseded by a later OPTIONS directive or by the options list for the job These job options can specify any of the following items for the relevant jobs Keyword settings in the gen section of the Jaguar input file Paths and names of data files such as the basis set file or the grid file Sections to remove from the template input file for example the guess section if you are changing basis sets e Substitution of a specified number or string for one already in the template input file The format for each of these options and an example of each kind are shown in Table 10 5 Option assignments must n
494. the DFT energies was 0 72 kcal mol while the RMS error using the default LMP2 method was 0 34 kcal mol Other options are provided to control the optimization process Jaguar 7 0 User Manual Chapter 3 Options Jaguar provides a wide range of options for performing different kinds of calculations for controlling the convergence of calculations and for controlling the output of calculations Most of these options can be set in the various tabs of the Jaguar panel The options that are common to nearly all calculations are set in the following six tabs Molecule charge spin symmetry basis set Theory HF DFT LMP2 GVB GVB LMP2 CIS restricted unrestricted SCF SCF SCF convergence Properties frequencies surfaces ESP charges Mulliken populations NBO analysis multipole moments polarizabilities Solvation solvent reference energy Output printout options output files The remaining tabs that can appear in the Jaguar panel vary according to the task Optimiza tion Transition State IRC Scan These tabs are described in Chapter 4 along with other infor mation about optimizations and scans Output options are described in Chapter 5 This chapter describes the settings that can be made in the Molecule Theory SCF Properties and Solvation tabs The footnotes in this chapter indicate the Jaguar input file keywords and sections that corre spond to settings made in the GUI If you are working from the
495. the Gaussian functions that make up the basis set Keyword ip12 2 in the gen section Keyword ip192 2 in the gen section Keyword ip18 2 in the gen section Keyword ip19 2 in the gen section Keyword ip1 2 in the gen section No Di A Jaguar 7 0 User Manual 123 Chapter 5 Output 124 Gaussian function list derivatives By selecting this option you can print out information about the derivatives of the basis set functions in terms of primitive Gaussians The format and information is the same as that discussed for the Gaussian function list basis set option immediately above 5 5 File Output Options The options available in the Output tab of the Jaguar panel under Write input files in the selected formats are described in this section These options are presented as a list from which you can select multiple items with the SHIFT and CTRL keys These output options generate additional files For each of the options described below the relevant file appears in the same directory as the output file Each file name is in the form jobname suffix where the different suffixes for each kind of file are described below If you make a setting in the Output tab the output from the program pre lists the non default options chosen This output appears above the molecular geometry output from pre and gives the non default values of the keywords referred to in footnotes in this section Gaussian input
496. the Molecule tab you can choose a basis set from the three option menus labeled Basis Set Polarization and Diffuse The Basis Set option menu provides access to all the basis sets available to Jaguar If an option or menu is dimmed it is incompatible with the rest of your input for instance the basis set could be missing basis functions for some atom or atoms in your molecule Basis sets that do not have pseudospectral grids and dealiasing func tions are listed in italics in the Basis Set option menu If you do not choose a basis set for a calculation Jaguar uses the 6 31G basis set if 6 31G basis functions are available for all atoms in the input and otherwise uses the LACVP basis set by default These basis sets are described in more detail below The Polarization option menu provides the choices none and In general the option places polarization functions on all atoms except for transition metals and the option places polarization functions on all atoms except for transition metals H and He The tables below describe in detail the atoms that have polarization functions in each basis set The correlation consistent basis sets cc pVnZ are intrinsically polarized The Diffuse option menu provides the choices and The option places diffuse functions on all atoms while the option places diffuse functions on all atoms except H and He Diffuse functions are useful for calculations on van der Waals complexes or
497. the calculation The ordering of the sets used for each grid type is determined by the parameters named dcoarse dmedium and so on which are specified in the gen section of the input file By default the coarse grid is listed first then the medium fine ultrafine and gradient grids in that order The second number in the second line gives the number of ranges described in each of these dealiasing function sets The ranges correspond to particular RwR blocks for the calculation One of these ranges is the long range basically covering the whole molecule another is the home atom range which actually only includes the relevant atom itself and the rest are increasingly large neighbor ranges The number of ranges should currently not exceed 10 The sample file s second line indicates that for each basis set five dealiasing function sets are spec ified for each atom and that each of these sets contains dealiasing functions for a total of six 1 To see this connectivity information for a system set ip12 2 in the gen section Jaguar 7 0 User Manual Chapter 9 Other Jaguar Files ranges the long range functions the functions for the home atom and the functions for four other neighbor ranges The distances defining the neighbor ranges are set in the next line of real values in units of bohr Note however that generally only the third neighbor range is actually used The first distance specifies that if the basis function whose coef
498. the electric field and r is the electron position The contribution due to the interaction between the field and each nucleus of position r and charge q is q E r The efields section can contain more than one line describing several different fields In that case the calculations for each given field will be performed in turn Up to 100 electric fields can be specified 8 13 The ham Section By using the ham section and setting the gen section calculation keyword ihamtyp to 3 you can specify the exact coefficients used to calculate the electronic energy for open shell calcula tions The electronic energy is given by the equation E Abt Y Git Kuba L ij where the sums are over orbitals 22 The number of electron pairs per orbital in each orbital i is indicated by f which can be listed in the ham section and the one electron Hamiltonian for that orbital is given by A The terms a and bj are coefficients which can also be specified in the ham section and the J and K terms are Coulomb and exchange terms for pairs of orbitals i and j Orbitals which have the same a and b coefficients and number of electron pairs f are considered to be in the same shell The first line in the ham section should indicate the number of core orbitals for the molecule Next each shell is described in turn The first line of each shell description should contain two numbers the first an integer indicating the number of orbitals in that shell
499. the environment variable SCHRODINGER to point to the installation directory on that machine This is the directory Jaguar 7 0 User Manual 283 Chapter 11 Troubleshooting 284 containing Jaguar version 7 0 which is in a subdirectory called jaguar vxxxxx where xxxxx is the five digit version number To check whether the SCHRODINGER environment variable is set enter the command echo SCHRODINGI D H If the output from this command is a directory containing Jaguar you can skip the rest of this subsection If you determine that the SCHRODINGER environment variable has not been defined you must set it If you don t know where the installation directory is ask the person who installed Jaguar Then depending on your shell enter one of the following commands csh tesh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory You should also set the SCHRODINGER environment variable in your shell startup file in the cshrc file in your home directory if you are running C shell for instance by adding the setenv or export command to the file so that it is defined for any shell that is used whether interactively or in a batch job 11 1 2 Including the jaguar Command in Your Path The command jaguar is actually a short script that finds the appropriate version of Jaguar to run and passes on any relevant options to the main Jaguar program If you have set the SCHRO
500. the force upon it in the x y and z directions The x y and z components of the total force on the molecule are listed in the last line and provide a judge of how accurate the force calculations are in most cases since they should generally be zero An example of this force table for a water molecule optimization follows forces hartrees bohr total atom label x y Zz i 0 0 000000E 00 0 000000E 00 2 620407E 05 Jaguar 7 0 User Manual 99 Chapter 5 Output 100 2 H1 0 000000E 00 6 462331E 05 1 291533E 04 3 H2 0 000000E 00 6 462331E 05 1 291533E 04 total 0 000000E 00 0 000000E 00 2 321025E 04 When force calculations or optimizations of a system s minimum energy structure or transition state are performed at the LMP2 level the program derib never runs Instead forces are calculated by the programs lmp2der lmp2gda and lmp2gdb The last of these programs provides a table of output listing the forces on each atom in the same format as the sample table above For geometry optimizations Jaguar prints bond length and angle information in the output from the program pre If you have constrained bond lengths or angles of the geometry so that they are frozen during the optimization as described in Section 4 2 on page 70 the constraints are also listed in the pre output At the end of the first SCF calculation the programs der1a rwr and der1b run calculating the forces felt by each atom in the unoptimized geometry and w
501. ther orbitals Coulomb and exchange opera tors At the beginning of each SCF iteration the scf program is provided with a set of proposed natural orbitals and a set of CI coefficients that dictate the contribution of each natural orbital to the GVB orbitals For that set of GVB natural orbitals the program first solves for revised CI coefficients by evaluating the Coulomb and exchange matrix elements for those orbitals and diagonalizing the two by two matrices Y in the basis of the two natural orbitals in pair p as described by these equations Yee Co 13a N 1 vb 2 P Ypg pg Mpg pg 2 ps pet gt Cas 24 ag pg Kag pg 13b q p N vb 2 i gt Col Zon pg Kqu pg q p N 1 vb 2 P Ypu pu h pu pu 27 pu pu Y C QJ qg pu E 5 m 13c q p N yb 2 Y EE Kye pu q p 1 p _yp _l Ypg pu z Y ge 7K pg pu 13d In practice since the CI coefficients are mutually interdependent they are determined using a self consistent iterative procedure Jaguar 7 0 User Manual Chapter 7 Theory Next holding the CI coefficients fixed the program evaluates the energy and the Fock matrix and adjusts the basis set coefficients describing the GVB natural orbitals accordingly in basi cally the same manner used for the usual HF treatment The revised orbitals and CI coefficients are then used in the next SCF iteration and the process continues until both the GVB natural orbitals and the CI coefficients have converged
502. this keyword sets these two quantities For solvated geometry optimizations the trust keyword which is described in Section 8 5 10 on page 177 has a default value of 0 1 instead of its usual default of 0 3 Table 8 24 Keywords for solvation calculations Keyword Value Description isolv 0 Do not perform a solvation calculation 2 Perform a solvation calculation using a Poisson Boltzmann solver 5 Perform a solvation calculation using SM6 This is the only solvation keyword that should be specified when performing SM6 calculations icavity 0 Do not include solute cavity energy term in solvation calculation 1 Include solute cavity energy term default when the solvent is water 2 Force calculation of cavity energy term isurf 0 Do not include first shell correction factor term in solvation energy 1 Include first shell correction factor term in solvation energy default for most calculations in water turns on Lewis dot keyword ivanset 1 by default ivanset 0 Do not set van der Waals radii according to Lewis dot structure Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 24 Keywords for solvation calculations Continued Keyword Value Description 1 Set van der Waals radii according to Lewis dot structure lewstr 1st structure by default see Section 8 5 6 on page 165 and Section 9 6 on page 254 kesep 0 Combine terms for all one electron matrices 1 Keep kinetic energy terms nu
503. thod to be used This basis set information can be found in Section 3 2 on page 30 A warning is displayed if you choose a non pseudospectral calculation The reference wave function is produced through a localization of the usual Hartree Fock reference wave function using a unitary transformation of the occupied canonical Hartree Fock orbitals This localization procedure does not change the reference energy The default localization procedure is Pipek Mezey 62 localization but you can choose Boys 61 local 44 Keyword loclmp2v 2 in the gen section Jaguar 7 0 User Manual 41 Chapter 3 Options 42 ization or an alternate Pipek Mezey localization 6 see Section 8 5 7 on page 167 These schemes are available from the Valence localization method option menu In LMP2 unlike in canonical MP2 the correlating virtual space for each occupied orbital is limited to those orbitals that are localized on the atoms of the local occupied Hartree Fock orbital The localization of the occupied orbitals makes this limitation of the virtual space a good approximation and leads to a reduction in the basis set superposition error In the limit that all local virtual orbitals are assigned to every occupied orbital the local MP2 method and the canonical MP2 method are exactly equivalent All calculation types available for LMP2 wave functions are also available with the local local MP2 method which allows you to treat only some
504. thout performing SCF or other later calculations lewstr 0 Print all Lewis dot structures if lewdot 1 or 1 gt 0 Use structure number lewstr for output and or setting GVB pairs lewstr 1 by default if igvball gt 0 igvball 0 Do not select any GVB pairs based on Lewis dot structure 1 Select GVB pairs for any atoms according to igvbsel and Lewis dot structure lewstr Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 6 Keywords for evaluation of Lewis dot structures and application of that information to GVB pair settings Continued Keyword Value Description 2 Select heteroatom GVB pairs only according to igvbsel and Lewis dot structure lewstr heteroatom pairs are all pairs whose atoms are differ ent elements except for C H pairs igvbsel Select only sigma GVB pairs Select only pi and second pi GVB pairs Select only sigma pi and second pi GVB pairs Select only lone GVB pairs Select only lone and sigma GVB pairs Select only lone pi and second pi GVB pairs N DBD Ww A U N Select sigma pi second pi and lone GVB pairs default when igvball gt 0 8 5 7 LMP2 Keywords The mp2 keyword allows you to request a local M gller Plesset perturbation theory LMP2 calculation By default LMP2 is off For more information on the local MP2 method see Section 3 5 on page 40 and Section 7 4 on page 149 LMP2 keywords are given in Table 8 7 LMP2 calculations require a basis set that a
505. tion functional xcornl1 Perdew 1986 non local gradient correction xcornl2 Lee Yang Parr local and nonlocal correlation functional xcornl3 HCTH407 local and nonlocal correlation functional Jaguar 7 0 User Manual 175 Chapter 8 The Jaguar Input File 176 Table 8 15 Functional coefficient keywords Continued Keyword Corresponding Functional or Exact Exchange xcornl4 Perdew Wang GGA II 1991 nonlocal correlation functional xcornl6 Becke 1998 B98 local and nonlocal correlation functional xcornl7 Schmider and Becke 1998 SB98 local and nonlocal correlation functional xcornl8 B97 1 local and nonlocal correlation functional xcornl9 PBE nonlocal correlation functional xcornl11 B95 nonlocal correlation functional 41 xcornl12 B95 as modified by Zhao and Truhlar for PWB6K xcornl13 B95 as modified by Zhao and Truhlar for PW6B95 xcornl14 M05 local and non local exchange xcornl15 M05 2X local and non local exchange For DFT jobs the keyword vshift is set to 0 2 for hybrid methods or 0 3 for non hybrid methods by default and the keyword idenavg is set to 1 by default to aid convergence More complete descriptions and references for each DFT functional and hybrid are given in Section 3 3 on page 35 8 5 9 CIS and TDDFT Keywords The configuration interaction singles CIS and time dependent density functional theory TDDFT methods can be used after a closed shell SCF calculation to generate information on excited states The o
506. tion scheme used restricts the number of CI coefficients in the RCI calculation to n where n is the number of GVB pairs yet is in excellent agreement with a fully uncontracted CI which by contrast would contain 2 CI coefficients the number of uncontracted determinants The GVB RCI program within Jaguar generates a correlated wave function from intra pair excitations of the GVB reference wave function described in Section 7 2 using a highly effec tive contraction procedure to reduce the length of the CI expansions The program employs the pseudospectral method to speed up integral evaluation and systematically includes the most important configurations to make the calculation more practical with minimal loss of accuracy relative to the fully uncontracted expansion The spatial states for an RCI pair are constructed from the same natural orbitals as those used for the GVB reference wave function y and Wa but in addition to the GVB spatial state from Equation 6 rewritten here Jaguar 7 0 User Manual 147 Chapter 7 Theory 148 2 2 Spo CygWpg C puWpu 14a the RCI spatial states include the orthogonal complements es and o2 Epi VpgV pu 14b 2 2 Bu 7 Cpu pg Cog V p 140 Just as the GVB method allows the user to correlate particular electron pairs for maximal effi ciency the RCI treatment can be applied to any user specified subset of the GVB pairs A GVB mean field procedure is then used to evaluate
507. tive The third line is made up of five items the atom label for atom 3 the identifier of one of the previous atoms the distance between this atom and atom 3 the identifier of the other previous atom and the angle defined by the three atoms In this example N1 C2 N1 1 4589 c3 C2 1 5203 NI 115 32 the final line states that atoms C3 and C2 are separated by 1 5203 A and that the C3 C2 NI bond angle is 115 32 The bond angle must be between 0 and 180 inclusive The third atom C3 in this case is placed in the xz plane positive x The fourth line contains seven items the atom label for atom 4 an atom identifier the distance between this atom and atom 4 a second atom identifier the angle defined by these three atoms a third atom identifier and a torsional angle In this example N1 C2 N1 1 4589 C3 C2 1 5203 NI 115 32 04 C3 1 2036 C2 126 28 N1 150 0 the last line states that atoms O4 and C3 are 1 2036 units apart that the O4 C3 C2 bond angle is 126 28 and that the torsional angle defined by O4 C3 C2 NI is 150 0 This information is sufficient to uniquely determine a position for O4 If the first three atoms in the torsional angle definition were collinear or very nearly collinear O4 s position would be poorly defined You should avoid defining torsional angles relative to three collinear or nearly collinear angles In such a case you should use dummy atoms to define the torsional angle see Section 2 4 5 on page 13
508. to M05 but parametrized for nonmetals by Zhao Schultz and Truhlar 52 53 MO6 HF 7 Zhao and Truhlar functional with full HF exchange and M06 local functionals that eliminates long range self interaction 55 MO06 Zhao and Truhlar functional parametrized with metallic systems for organome tallic and inorganometallic chemistry and noncovalent interactions 56 M06 2X Zhao and Truhlar functional parametrized for nonmetals for main group ther mochemistry kinetics noncovalent interactions and electronic excitation energies to valence and Rydberg states 56 Keyword dftname bhandhlyp in the gen section Keyword dftname x3lyp in the gen section Keyword dftname mpwlk in the gen section Keyword dftname mpwlpw 91 in the gen section Keyword dftname pwb6k in the gen section Keyword dftname pw6b95 in the gen section Keyword dftname m05 in the gen section Keyword dftname m05 2x in the gen section Keyword dftname m06 hf in the gen section Keyword dftname m06 in the gen section Keyword dftname m06 2x in the gen section Jaguar 7 0 User Manual 39 Chapter 3 Options 40 The names of the functionals in this list are valid values of the keyword dftname which you can use in the gen section of the input file to specify the functional The names are case insen sitive 3 4 Hartree Fock and CIS Settings In addition to selecting unrestricted UHF or spin restricte
509. to calculate the Hessian choose Quantum mechanical Do not use any of the other options from this menu because it is important to have an accurate Hessian If you precalculate the Hessian and read it in the symmetry of the transition state is used for the entire calculation If the IRC path breaks symmetry you should turn symmetry off in the Molecule tab If you calculate the Hessian as part of the IRC or MEP calculation symmetry is turned off in the Hessian evaluation and remains off for the remainder of the run IRC and MEP calculations can be run in either direction from the transition state You can select the direction of the scan from the Direction option menu The direction of the reaction coordinate can be defined by supplying the reactant structure and the product structure in the Structures section of the IRC tab These geometries are selected in the same way as for a tran sition state search see Section 4 3 2 on page 76 The same rules for atom numbering in the reactant and product structures apply as for transition state searches If you do not supply the reactant and product structures Jaguar defines the forward direction using the rules described in Section 8 5 12 on page 184 You can run an IRC scan from a point that is not a transition state by selecting Downhill from the Direction option men 27 and providing the geometry as if it were a transition state For these calculations you do not need an initial guess of the
510. tomic orbital space HF or molecular orbital space GVB ip123 Fock matrix in canonical orbital space ip149 GVB data f a b etc ip188 Debug printing for automatic cutoff convergence scheme ip201 Total electronic density integrated on the DFT grid a See text in this subsection for information on ip152 The keyword ipvirt determines how many of the virtual orbitals are printed in the output file and in the restart new input file Virtual orbitals are printed in order of increasing energy The virtual orbitals are obtained by diagonalizing Ho gt f 2J K where f is the fractional occupation of each orbital 1 for a closed shell If ipvirt 1 all virtual orbitals are printed in the output and restart files otherwise ipvirt virtual orbitals are printed if that many virtual orbitals exist By default ipvirt 10 Several possible formats and levels of information can be requested for each other keyword determining the orbitals printed The choice of keywords which are listed in Table 8 35 deter mines the stage or stages at which orbitals are printed the keyword values determine which orbitals are printed and the format of the printing These settings can generally also be made from the GUI as described in Section 5 6 on page 125 Table 8 35 Keywords that specify when to print orbitals Keyword Prints Orbitals ip100 For initial guess from before SCF generally redundant with ip105 ip101 In canonical orbital space each
511. tomic section should list sets of atomic input values Each of these sets is a free format table The first row of the table lists the keywords whose values are to be set for each atom This row is the column heading row Subsequent rows list the values for the keywords for each relevant atom For instance in the following atomic section amp atomic atom mass vdw2 H1 2 00 1 20 H2 2 00 1 20 atom vdw2 O 1 55 amp the keywords are atom the atom label or number mass the nuclear mass in amu and vdw2 the van der Waals radii for PBF solvation and the lines for the atoms H1 and H2 specify that these atoms have a nuclear mass of 2 00 amu deuterium and solvation van der Waals radii of 1 2 A while the line for atom O specifies a solvation van der Waals radius of 1 55 A for this atom It is not necessary to list information for atoms that are to be treated in the default manner Keywords are case insensitive Columns can be given in any order All entries in a row should be separated by one or more spaces or tabs but columns do not need to be aligned The atom column must be included in every set of atomic input values The atom identifiers can be either atom labels such as H1 or O in the example above or atom index numbers such as 2 for the second atom listed in the zmat input Atom label input is case sensitive If you do not want to set a value for a given atom you can use a or to indicate that the default value shoul
512. top Tep noryed wan 03 posn sjes stseq ay Ajroeds 0 noA smoje pIOMADY sISeq au SWO Y ENpIAIpU 10 eBesf Heys pue uonoung Buiseijeog puy siseg eg uorjeurogjur Surpuoq pue rrped juop eAoo sjuesoid pue sosn 1engef moy uo uorjulojur e1OUI 10J 59 oSed uo 7c 9 uoroog pue cc Fed dag pIOMADY AOD Y Sursn posuLYd oq ULO mper osau T I Jo MPA 3 nejop YUM ploMADY uoroes UF v SI IBJAOD MYM IIpel jUo EAOO MY JO WINS a SOW IBJAOD utu sso ST WY uooAgoq DOURISIP ou D popuog aq 0 poreprsuoo ae SUIOW OMY OP S IGRI Ul UAAIS ore popuoq e SWOJ YOTYA SUTLIOJOp 0 pesn rrped JUITPAOD aq posuvyo oq JOUULD sone osau SPY o qe Ul PASI oie suor no e QNS 10 trped quio no SISULNUT pue STEE Jop ULA AL suore nope2 UONPAIOS UI TIpe1 ISIYI sosn IeNSeL MOY UO uorguriojur IIOU 10J pcc 2ed uo 9 6 uonoeg sdnois euorpoung euros ur Int Aq pojsnfpe oq ueo pue Ig O dY O N O H siueure o oy 10 mper eur po ox ZMPA oY Sursn peSueqo oq ue pue pp 9 AQEL ur PASI ITE suonenop eo uoneA Os qd JO Irper SELM Jop UPA eur Jaguar 7 0 User Manual 222 The Jaguar Input File Chapter 8 SBIT SPET PLUT ESEE LET LLET OCFT O9 T LAYI VEST S8S T OLS T IU T ISS T 6ST 1g id c8 LL I8 92H OS8 hV o SL LL SO oan SLIM FELL LJH Ze Leipg gea SS TOTT OSC C secc OIcC OIL S TETT PUI PLET OSP T VOV T ISP TL 66V T OCSI
513. tory for the job at the end of the last completed Jaguar program writing over any previously generated restart in file for the job The file restart in contains the results from the run including the new geometry if the run that produced it was a geometry optimization This input file can therefore be used to restart the calculation At the end of the job the restart input file is copied to your local job directory under the name jobname 01 in unless that file already exists otherwise jobname 02 in or jobname 03 in and so on To turn off ip151 you must set it to 0 Setting ip472 2 writes structures at each step of a geometry optimization or an IRC scan to the Maestro formatted output mae file The other file output keywords control whether files for various other programs such as GAMESS are written out during a Jaguar job The effect of setting each of these keywords to 2 is shown in Table 8 33 Many of these options can be turned on from the GUI as described in Section 5 5 on page 124 Additional settings are available for ip160 and ip165 When ip165 3 the SPARTAN 4 0 archive file is written to the local job directory as jobname arc When ip160 3 an initial guess is included in the gau file generated by the run by default gau files generated for GVB calculations include initial guesses but those for other calculations do not If SCF itera tions are performed the initial guess for the gau file is obtained from the re
514. trix elements from the previous iteration to the current one Finally the maximum DIIS error column provides a measure of convergence by listing the maximum element of the DUS error vector For HF calculations the DHS error vector is given by FDS SDF in atomic orbital space where F D and S are the Fock density and overlap matrices respectively For open shell and GVB cases the definition of the error vector is given in reference 11 If you are not running a default single point Hartree Fock calculation the log file generally contains information generated from other Jaguar programs used for the run as well This information is often a summary of what is written to the Jaguar output file For a more detailed description of the information in the log file see the previous sections of this chapter After all the individual programs necessary for that job have finished running a note appears in the log file listing the name and location of the output file When the job is finished this too is noted in the log file Jaguar 7 0 User Manual 129 130 Jaguar 7 0 User Manual Chapter 6 Using Jaguar This chapter provides some information on how to use Jaguar to obtain the results you want It includes information on setting up an initial guess especially for transition metal systems convergence of SCF and geometry optimizations setting up certain kinds of calculations restarting jobs and using Maestro and Jaguar to set up GAU
515. tropy S enthalpy H internal energy U and Gibbs free energy are then listed for the specified pressure and temperatures as well as at 0 K Here is an example of this output from a vibrational frequency calculation on FOOF start of program freq harmonic frequencies in cm 1 reduced masses in amu force constants in mDyne A and normal modes in cartesian coordinates IR intensities in km mol frequencies 226 83 587 12 708 27 994 11 1063 07 1086 36 intensities 769 00 6 20 6 85 56 95 18 20 reduc mass 5 96 4 34 4 66 7 85 4 37 4 40 force const 18 88 1 38 4 57 2 91 3 06 F1 X 03713 07085 05263 01504 10332 10413 F1 Y 07738 08093 07570 00294 00858 01121 F1 Z 11257 01960 00381 00291 00007 00142 02 X 03630 04451 02646 05071 13148 12893 02 X 00653 00113 11356 16823 01169 04865 02 Z 07806 12275 08708 00749 00934 01566 03 X 07467 12140 LAL 03829 00279 01163 03 Y 02320 01992 07655 17175 02320 01800 03 Z 03681 04285 05472 00584 13452 13276 FA X 13055 00611 01869 00459 00502 00537 FA Y 05236 09865 08436 00590 01826 01460 FA Z 01586 04767 03106 01413 10532 10001 Thermochemical properties at 1 0000 atm Jaguar 7 0 User Manual 115 Chapter 5 Output 116 rotational symmetry number 1 rotational temperatures K 1 075181 283392 256070 vibrational temperatures mode 1 2 3 4 5 6 temp K 326 36 844 73 1019 03 143
516. try and Physics Weast R C Ed 60th edition CRC Press Boca Raton FL 1979 Dielectric constants for 20 deg C were used Water s probe radius is set to 1 40 to reproduce solvation energies properly All other probe radii are calculated from r 3mA 4np ao A cm where r is the solvent probe radius in Angstroms m is the molecular mass obtained by dividing the molecular weight given in ref 67 in grams per mole by 6 02 x 10 A is the packing density and p is the density in g cm at 20 deg C obtained from ref 67 Finding the actual A would require a detailed knowledge of the structure of the liquid Currently all A values for these liquids are assumed to be 0 5 For FCC lattices A is 0 7405 and for BCC lattices A is 0 6802 Rapp A K Casewit C J Colwell K S Goddard W A Skiff W M J Am Chem Soc 1992 114 10024 Chirlian L E Francl M M J Comput Chem 1987 8 894 Woods R J Khalil M Pell W Moffat S H Smith V H Jr J Comput Chem 1990 11 297 Breneman C M Wiberg K B J Comput Chem 1990 11 361 Mayo S L Olafson B D Goddard W A III J Phys Chem 1990 94 8897 Mulliken R S J Chem Phys 1955 23 1833 Glendening E D Badenhoop J K Reed A E Carpenter J E Bohmann J A Morales C M Weinhold F NBO 5 0 Theoretical Chemistry Institute University of Wisconsin Madison WI 2001 Baker J Jarzecki A A Pulay P J
517. try optimizations in solution contain output in the formats described in the previous two subsections but the optimization output and the solvation calculation output alternates as the calculation proceeds First by default Jaguar computes a gas phase optimized geometry for which the output is the same as that described above for a standard optimization Next the SCRE procedure is used to compute a wave function for the solvated system as for a single point solvation energy calculation When the solvation energy has converged Jaguar runs the program pbf once more to get the solvation related gradient This opt output does not contain the usual solvent accessible surface area and cavity energy terms The programs der1a dsolv rwr and der1b then compute the forces with the force table in the der1b output in the usual manner and the program geopt computes the new molecular structure as usual For each new structure generated during the optimization Jaguar first performs the SCRF calculation then obtains the forces in solution and finally generates a new structure The calculation proceeds until the geometry optimization convergence criteria are reached The convergence criteria for optimizations in solution are three times larger than they are for optimizations in the gas phase For solvated geometry optimizations the solvation energy is computed as the difference between the energy of the optimized gas phase structure and the energy of the sol
518. ts are additional potential energy terms in the form of a harmonic potential with a given force constant k centered at an atom or on a particular internal coordinate value The constraint can include a region where the potential is zero inside the constrained area The form of the potential is as follows V k 2 d a d a k 2 d a d a 0 a d a For atomic Cartesian harmonic constraints the value of d is the distance from the atom For internal coordinate harmonic constraints bond length bond angle or dihedral angle the value of d is the difference between the coordinate value and its desired value d r c where r is the coordinate and c is the center or target value The constraint is then more like a dynamic constraint in which the coordinate is at the target value at the end of the optimization These extra potential energy terms are listed in the output and used to determine geometry convergence but they are not included in the final energy Harmonic constraints must be set in the coord section of the input file and can be set on the Cartesian position of an atom or on any bond length angle or dihedral angle To set a harmonic constraint adding hc or HC after the coordinate followed by the force constant If you want to specify a region of zero potential add the half width of this region a after the Jaguar 7 0 User Manual Chapter 4 Optimizations and Scans force constant If you want to specify a t
519. types for babel file format conversions Continued Format Keyword File Type unixyz UniChem XYZ file XYZ XYZ file xed XED file For either babel or babelg keyword settings you can use an optional extra extension for the file name by setting babel or babelg to a keyword in the form outext opt where opt is any extension you want to use For instance if you made the setting babel gzmat gau in a Jaguar input file called h2o in the resulting job would create a Gaussian input file called h20 gzmat gau You can also convert file formats from the command line using the jaguar babel and jagconvert utilities See Section 10 1 5 on page 269 for information on these utilities 8 5 21 Standard Output Keywords The keywords listed in Table 8 32 are the standard print options They are all set to 1 by default and the result is that none of the information that the keywords select is printed Many of the print options can be turned on from the GUI as described in Section 5 4 on page 121 The keyword setting ip6 3 provides much more detailed timing information than the setting ip6 2 Similarly the keyword setting ip192 3 provides more detailed output than ip192 2 the ip192 3 setting includes the Hessian The keyword setting kesep 1 which is normally part of a solvation calculation see Table 8 24 on page 186 causes the virial ratio V T to be printed out at the end of each SCF calculation Table 8 32 Output keywords and their setting
520. uar 7 0 User Manual References 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 Frisch M J Trucks G W Head Gordon M Gill P M W Wong M W Foresman J B Johnson B G Schlegel H B Robb M A Replogle E S Gomperts R Andres J L Raghavachari K Binkley J S Gonzalez C Martin R L Fox D J DeFrees D J Baker J Stewart J J P Pople J A GAUSSIAN 92 Gaussian Inc Pittsburgh PA 1992 Babel version 1 6 copyright 1992 96 W Patrick Walters and Matthew T Stahl AII Rights Reserved Permission of authors granted to incorporate Babel into Jaguar Dunietz B D Murphy R B Friesner R A Calculation of enthalpies of formation by a multi configurational localized perturbation theory application for closed shell cases J Chem Phys 1999 110 1921 Kaminski G A Maple J R Murphy R B Braden D A Friesner R A J Chem Theory Comput 2005 1 248 Boys S E Bernardi E Mol Phys 1970 19 553 Hirata S Head Gordon M Chem Phys Lett 1999 314 291 Becke A D J Chem Phys 1993 98 1372 Becke A D J Chem Phys 1993 98 5648 Stephens P J Devlin F J Chabalowski C E Frisch M J J Phys Chem 1994 96 11623 Slater J C Quantum Theory of Molecules and Solids Vol 4 The Self Consistent Field for Molecules and Solids McGraw Hill New York 1974 Vosko S H W
521. uar Files Table 9 1 Number of points per angular shell and degree of the highest spherical harmonic exactly integrated by grids specified by various entries on the angular grid line Continued Entry VD 00 N QN tA 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Points 18 18 24 26 38 38 42 44 44 50 54 56 60 60 78 78 86 90 90 110 116 146 146 194 302 434 Degree VD WD O O O N UA UA a LA N N re be ben Fe ben ke be ke ke ben Fe Y a Un O U NO O N N TT DD U ra ra ra ra rn Reference for Grid Un 5 1 Albrecht amp Collatz p 294 150 Un 5 1 Albrecht amp Collatz p 294 150 Un 5 4 Stroud p 295 150 Un 7 1 Albrecht amp Collatz p 295 150 9 1 Lebedev 151 9 1 Lebedev 151 9 2 Lebedev 151 9 3 Lebedev 151 9 4 Lebedev 151 U3 11 1 McLaren p 301 150 11 1 Lebedev 151 11 2 Lebedev 151 U3 11 2 Stroud p 301 150 11 3 Lebedev 151 11 3 Lebedev 151 13 2 Lebedev 151 13 3 Lebedev 151 15 1 Lebedev 151 15 2 Lebedev 151 15 2 Lebedev 151 17 1 Lebedev 151 17 2 Lebedev 151 19 Lebedev 152 19 Lebedev 152 23 Lebedev 152 29 Lebedev 153 Lebedev 154 Jaguar 7 0 User Manual 251 Chapter 9 Other Jaguar Files 252 9 5 The Cutoff File The cutoff file specifies parameters to be used for the various iterations of an SCF calculation The file to be used is dete
522. ucture its ycoor and zcoor values might change but their values for one hydrogen atom would always be the same as those for the other hydrogen atom so the molecule would retain C symmetry The variable settings can also be separated from the coordinates by a line containing the text Z variables For instance the following input is equivalent to the previous example O 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor Z variables ycoor 0 753108 zcoor 0 454006 Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro Note that if Cartesian input with variables is used for an optimization Jaguar performs the optimization using Cartesian coordinates instead of generating redundant internal coordinates and the optimization will not make use of molecular symmetry 2 4 8 Constraining Cartesian Coordinates As described in the previous section you can force Cartesian coordinates to remain the same as each other during an optimization by using variables You can also specify Cartesian coordi nates that should be frozen during a geometry optimization by adding a sign after the coor dinate values For example if you add constraints to the zcoor variables in the water input example as listed below 0 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 and perform a geometry optimization on this molecule the H atoms would be all
523. uency mode with the most negative eigen value of the Hessian is used to define the forward direction The phase of the eigenvector is chosen so that the largest coefficient is positive and the forward direction is the direc tion that increases the coordinate for the largest coefficient IRC calculations can be done in either Cartesian coordinates specified with intopt 0 or redundant internal coordinates intopt 1 which is the default IRC in anything but the downhill mode requires a Hessian which must either be entered in the hess section or calculated analytically The latter is specified with inhess 4 in the gen section Initial guess Hessians are not useful as they do not have any imaginary frequencies If a Hessian is entered in the hess section whether directly or from a restart file for a calculation Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 23 Keywords for IRC calculations Keyword Value Description irc 0 Do not do IRC calculation 1 Do IRC calculation with non mass weighted coordinates minimum energy path scan 2 Do IRC with mass weighted coordinates ircemode forward Find IRC points in forward direction from the transition state reverse Find IRC points in reverse direction from the transition state downhill Find IRC points by moving downhill from an initial geometry that is not a transition state both Find IRC points in both forward and reverse directions
524. ulation with the C2 C3 bond pair delocalized over C1 and C4 as well as over C2 and C3 amp gen mp2 3 idelocv 2 amp amp lmp2 C2 C3 CL C4 amp For QST guided transition state searches with LMP2 wave functions LMP2 delocalization will automatically be performed over neighboring atoms for any bonds present in one structure and not in another unless the input file contains the gen section keyword setting idelocv 0 Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File 8 8 The atomic Section The atomic section allows you to specify data for different atoms in a molecule This data can include basis sets for each individual atom or atomic masses a feature that allows isotope calculations You can also use the atomic section to define groups of atoms called fragments where each fragment can then be converted to dummy atoms or counterpoise atoms or used to define a part of the system for which you want to compute a numerical Hessian Restart files may include atomic sections as well in order to keep information about charge fitting or other properties calculated previously In addition atomic sections can be used to supply information about transition metal containing systems that is used to generate high quality initial guesses for these systems See Section 6 1 3 on page 133 for more information on using atomic sections in this manner 8 8 1 General Format of the atomic Section After the amp atomic line the a
525. ule Theory scr Properties Solvation Output Accuracy level Quick zd Convergence criteria Maximum iterations 48 Energy change Se 05 hartree RMS density matrix change se 06 Convergence methods SCF level shift 0 00 hartree Thermal smearing FON m Initial temperature 10000 00 K Convergence scheme DIS 41 Force convergence use with caution see iacscf keyword in the manual Orhitals 4 Fixed symmetry populations Final localization None l Job GVB 6 31G Single Point Energy Frequencies Start Read Write Edit Reset Close Help Figure 3 5 The SCF tab The default energy convergence criterion which can be set in the Energy change text box is 5 0x10 Hartrees When the change in total energy on consecutive iterations is less than this value the energy is converged For polarizability calculations the default is 1 0x10 Hartrees If the energy difference is less than 1 of the previous energy difference however this conver gence criterion is overridden for that iteration and the calculation continues The default density convergence criterion which can be set in the RMS density matrix change text box is 5 0x10 When the RMS difference in density matrix elements between 55 Keyword econv in the gen section 56 Keyword dconv in the gen section Jaguar 7 0 User Manual Chapter 3 Options two it
526. ult is SCHRODINGER mmshare vversion data jaguar pka_match xml o filename Specify a Maestro output file s solvent Specify a solvent The solvent must be one for which pK parameters are available Jaguar 7 0 User Manual 317 Chapter 13 The pK Prediction Module 318 As an example if Jaguar has calculated the pK for an aniline and you want to see what the pK would be if it had been corrected using the parameters for primary amines you could change into the jobname_pka directory and run the following command SSCHRODINGER utilities jaguar pka f primary amine jobname in The output looks something like this This molecule was specified by the user as a primary amine Correction factors have been applied and have an RMSD of 0 5 The pKa for 2clphnh2 is 5 7 13 5 Developing Your Own pK Correction Parameters If you want to develop your own pK parameters you can do so by adding information to the file that contains the parameters that Jaguar uses to correct its calculated pK values SSCHRODINGER mmshare vversion data jaguar pka match xml This file also contains the SMARTS patterns that enable Jaguar to recognize functional groups You can thus extend Jaguar s ability to calculate pK values for new functional groups simply by adding the appropriate SMARTS patterns and correction parameters to this file A description of the XML file format standard is beyond the scope of this document but the format is
527. und for each iteration The Lowest non torsional mode and Lowest bond stretch mode 20 Keyword itrvec 0 in the gen section 21 Keyword itrvec 1 in the gen section 22 Keyword itrvec 2 in the gen section 23 Keyword itrvec gt 0 in the gen section 24 Keyword itrvec 5 in the gen section Jaguar 7 0 User Manual 77 Chapter 4 Optimizations and Scans 78 options can be useful for steering the optimizer to a particular type of transition state for instance for a study of a bond breaking reaction you can avoid converging to a torsional tran sition state by choosing Lowest bond stretch mode If you know the index number of the eigenvector along which you would like to minimize a particular bond stretch for instance you can make the optimizer follow that eigenvector by choosing User selected eigenvector and specifying the eigenvector number in the Eigenvector text box gt You can identify the index number by running one geometry optimization iteration see Section 4 1 1 on page 68 for more information and examining the output summary of the Hessian eigenvectors which indicates the dominant internal coordinates and their coefficients for each eigenvector You can also determine the eigenvector to follow from a vibrational frequency calculation However because different mass weighting schemes are used in vibrational frequency calcula tions and transition state searches it is possible for the two calculation
528. ure files 10 2 3 1 Pipelined Jobs Suppose you have ten different molecules and you want to optimize the geometry of each one at the B3LYP 6 31G level of theory and then do two single point energy calculations on the optimized geometry one using B3LYP 6 311 G and the other using LMP2 6 311 G The batch file for this process given below would read in each molecular geometry from an existing input file make the necessary keyword changes and perform the calculations B3LYP 6 31G geometry optimization SJOB SJOB_dft_opt igeopt 1 basis 6 31g dftname b3lyp remove igeopt setting for the following single point calculations and change basis set to 6 311 G OPTIONS igeopt NONE basis 6 311 g run B3LYP single point calculation SJOB dft opt 01 JOB dft sp change level of theory to LMP2 and run single point calculation SJOB dft opt 01 JOB lmp2 sp dftname NONE mp2 3 10 2 3 Running Jobs from Input in a Specified Directory The script below runs jobs for a set of input files in a specified directory using two different sets of options and places the output in subdirectories of the launch directory Define protocol 1 OPTIONS basis midi dftname x3lyp icfit 1 Create the job directory and cd into it All job files will be written to this directory if WORKDIR and OUTDIR are set to the same directory name WORKDIR protocoll OUTDIR protocoll Get the input files append protol to each add the OPTIONS
529. used to store temporary files A subdirectory with the given job name h2o for example is created within the temporary directory and the files from the calculation are stored in this subdirectory If the subdirectory and directory do not have sufficient disk space for the job the job fails If the temporary directory does not exist you should create it or choose a directory which already exists If none of the temporary directory choices already exist and you do not want to create the necessary directories you can change the schrodinger hosts file so that the option menu offers you different choices see Section 2 1 of the Job Control Guide 2 9 3 Starting and Monitoring Jobs When you are satisfied with the settings start the job by clicking Start The Monitor panel opens and displays the Jaguar log file for the job As the job runs this file is updated If you close the Monitor panel the updating ceases You can reopen the panel later by choosing Monitor Jobs from the Applications menu To monitor the job again select it in the table and click Monitor See the Chapter 5 of the Job Control Guide for more information on job control and monitoring Any additional jobs that you submit run concurrently If you exit Maestro any Jaguar jobs still running continue to run to completion 2 10 Running Jaguar Batch Jobs You can run multiple Jaguar calculations in a single run using Jaguar batch scripts Some of the kinds of calculations you can
530. ut file is described in Chapter 5 2 12 J2 Theory Calculations If you want to calculate energies accurately you can perform J2 theory calculations 27 using a predefined batch script The J2 batch script performs a B3LYP 6 31G geometry optimiza tion and frequency calculation followed by single point GVB LMP2 calculations using the cc pvtz f and cc pvtz basis sets at the B3LYP optimized geometries These single point calculations are used to determine a basis set correction energy A parameterized electron pair correction energy is also added The final J2 energy is an absolute enthalpy at 298K The finite temperature effects are calculated from the B3LYP frequencies The J2 results do not include a standard heat of formation because the relevant calculations for the constituent atoms are not made J2 theory calculations cannot be performed for structures containing atoms that are heavier than Ar To run J2 theory calculations select J2 from the Jaguar submenu of the Applications menu The Jaguar panel has only the Molecule and SCF tabs because all other input is predefined When you have selected the structures and made any settings click Start You can also use the jaguar j2 command to run the calculation from the command line jaguar j2 options input files This command executes jaguar batch You can run the calculation on a remote host or in parallel by specifying the relevant command options See Section 10 2 on page 272 for deta
531. utput includes energies oscillator strengths and transition dipole moments for excitations from the ground state The keywords used to control the CIS or TDDFT calculation are listed in Table 8 16 A TDDFT calculation is performed if a density functional has been specified otherwise a CIS calculation is performed The rest of the calculation should be set up as a closed shell SCF calculation You should not normally need to set nrestart because the program determines how many iter ations it can do with the amount of memory available Jaguar 7 0 User Manual Chapter 8 The Jaguar Input File Table 8 16 Keywords for CIS and TDDFT calculations Keyword Value Description icis 0 Do not do a CIS or TDDFT calculation 1 Do a CIS or TDDFT calculation nroot gt 0 Number of roots to find Default value is 1 dconvci 1 0e 2 Convergence criterion for the norm of the residual vector default is 1e 5 for a non pseudospectral calculation econvci 1 0e 5 Convergence criterion for the change in energy default is 1e 8 for a non pseudospectral calculation nrestart gt 0 Number of iterations before restarting 0 Determine number of iterations before restarting automatically maxciit 32 Maximum number of iterations used 8 5 10 Geometry Optimization and Transition State Keywords Many of the keyword settings for optimization of minimum energy structures and transition states described in this subsection can be made from the GUI as descr
532. vated struc ture that was optimized in solution 5 3 7 Properties If you make any non default selections from the Properties tab the program ch runs and writes the results to the output file after the SCF iterations if any 5 3 7 1 Multipole Moments and Charge Fitting When multipole moments are calculated the x y and z components of the dipole moment and the total magnitude of the dipole moment Uu are reported in debye followed by information on any requested higher order moments and the corresponding traceless higher order moment tensors An example of the output for the dipole and quadrupole moments of water follows Jaguar 7 0 User Manual 109 Chapter 5 Output 110 Moments from quantum mechanical wave function Dipole Moments Debye X 0 0000 Y 2 1470 Z 0 0000 Tot 2 1470 Quadrupole Moments Debye Ang XX 4 0828 YY 5 7670 ZZ 7 1340 XY 0 0000 XZ 0 0000 YZ 0 0000 Traceless Quadrupole Moments Debye Ang XX YY 1 6843 2ZZ XX YY 4 4182 XY 0 0000 XZ 0 0000 YZ 0 0000 If electrostatic potential charge fitting to atomic centers is performed the output lists the number of grid points from the charge grid which is used for the charge fit It then describes the constraint or constraints for the fit followed by the calculated atomic charges and their sum The root mean square error of the charge fitting is also reported this error is calculated from examining the Coulomb field at each grid point that
533. vens 296 PATH csessessssteisasatenceassiessvicissacassen 284 294 298 REMOTE JAGUAR EXEC 298 REMOTE MMSHARE EXEC 298 RSHCOMMAND eerte 294 296 SCHRODINGER sssssssssesseiereenreeeeense 2 284 298 SCHRODINGER MPI FLAGS 299 302 SCHRODINGER NODEFILE 295 297 299 error messages can t open display sess 285 child process exited 300 command not found 284 285 loading shared libraries 5 299 login incorrect 288 memory related wea 289 permission denied von ZO temp directory 286 unknown service eee 286 ESP see electrostatic potential exchange corrections in pseudospectral calculations eee tt teen 254 exchange operator K keyword for per iteration output 208 keywords for calculation 195 obtaining i o information for 122 pseudospectral assembly of 142 143 excited state calculations CIS SCR p 40 keysvordss eene tini Gu e rette 176 TDDET settings nct tienen 35 executable directory sssse 92 266 selecting with jaguar run 267 execution hosts listing available sess 265 selecting un 22 200 troubleshooting 287 288 execution Dat 233 235 F file names 5er entes reas 23 file output options
534. vent 0 02160511215 E Total one electron terms 123 39806065860 F Electron nuclear 199 21812919134 G Electron solvent 0 03443064237 H Kinetic enso loss E x 75 85449917511 I Total two electron terms 38 01027466882 L Electronic energy 85 38778598978 E I N Total quantum mech energy 76 03617415619 A L O Gas phase energy 76 02364072535 P Solution phase energy 76 02607108661 Q R S Q Total solute energy 76 02334862596 N C G R Total solvent energy 0 00641276511 C 2 G 2 S Solute cavity energy 0 00369030447 U Reorganization energy 0 00029209939 Q O V Solvation energy 0 00243036126 P O SCFE SCF energy HF 76 03617415619 hartrees iterations 3 HOMO energy 0 49985 LUMO energy 0 22469 Orbital energies symmetry label 20 55803 Al 1 34624 Al 0 71287 B2 0 57176 Al 0 49985 B1 0 22469 A1 0 31901 B2 1 01892 B2 1 09275 A1 1 13045 A1 1 16509 B1 1 29393 B2 1 41452 A1 1 80375 A2 1 82851 A1 end of program scf As for any later solvation iterations the scf output begins with the calculation type and the table of energy results for each iteration skipping the list of information about the molecule s electrons and orbitals The energy information below the table includes several additional terms whose relations to each other are described with the usual alphabetic labe
535. very simple and resembles HTML in its use of tags to enclose sections of ordinary text The tags identify the purpose of the enclosed text For example the pK module informa tion for carboxylic acids looks like this functional group name carboxylic acid jaguar id 4 jaguar f1z 0 4451 f2z 0 2516 lt smarts gt 1 O0 CX3 0 lt smarts gt lt smarts gt OX1 CX3 0 lt smarts gt lt functional_group gt where name is a double quoted string that describes the functional group jaguar_id is an optional arbitrary index number for the functional group and 1 and 2 are the pK correction factors The first SMARTS pattern describes the acidic form of the molecule while the second SMARTS pattern describes the basic form of the molecule For more information on SMARTS patterns see the web page http www daylight com dayhtml doc theory theory smarts html 1 Please see the notice regarding third party programs and third party Web sites on the copyright page at the front of this manual Jaguar 7 0 User Manual Chapter 13 The pK Prediction Module The two pK correction factors 1 and 2 come from a linear fit of the calculated pK values to the experimental values for a particular training set of molecules f1 is the slope and 2 is the intercept You can perform linear fits with many commonly available software programs Here are some suggestions for selecting a set of molecules to use as a trainin
536. y G at standard temperature and pressure are performed by default whenever vibrational frequencies are calculated Rotational symmetry 97 Keyword irder 1 in the gen section Jaguar 7 0 User Manual Chapter 3 Options numbers which identify the number of orientations of a molecule which can be obtained from each other by rotation and zero point energies are also computed You can calculate these properties only if you are also computing vibrational frequencies With the settings in the Thermochemistry section you can set the temperatures and the pres sure used for calculations of these quantities The pressure in atm used for thermochemical calculations is 1 0 by default and the initial temperature in K is 298 15 by default To compute thermochemical properties at more than one temperature specify the differences between temperatures using the Increment to compute thermochemical properties in the Number of steps text box and the number of temperatures at which 101 text box The defaults are 10 00 K and 1 step meaning only one temperature is used By default thermochemical output is in units of kcal mol for H and G and cal mol K for C and S For output in units of kJ mol and J mol K instead select kJ mol under Output D 3 12 Surfaces By selecting Surfaces MO density potential in the Properties tab you can generate electro static potential electron density electron spin density 106 that
537. y and uses the results to refine the initial Hessian to be used for the opti mization To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the variable definition section For instance either of the following two input geometries will have the same effect a job that includes Hessian refinement will use both O H bonds and the H O H angle in the refinement O1 H2 O1 LE H3 O1 Lats H2 108 0 or 01 H2 O1 ohbond H3 O1 ohbond H2 108 0 ohbond 1 1 Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refine ment For example for the second water example shown above only two coordinates are actu ally refined the O H bond distance which is the same for both bonds and the H O H angle The same would be true for the first example if molecular symmetry were used for the job Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro _ Jaguar Read Filter fzonel dyall combiglide _ini Directories Files mbiglide temp3 prj 4 a N CH Launch Directory Working Directory Read as Geometry and settings Selection zonel dyall combiglide Figure 2 3 The Jaguar Read dialog box 2 5 Reading Files If you already have Jaguar input files containing geometries either with or with
538. ymm 0 in the gen section Jaguar 7 0 User Manual Chapter 2 Running Jaguar From Maestro Jaguar Write DIEN Filter fzonel dyall jaguar int Directories Files A PtCH2 01 in PtCH2 in PtCH2NR 01 in PtCH2NR in PtCH2NRHF 01 in PtCH2NRHF in PtCH2NRHFsurf in La l a Launch Directory Working Directory File Format Jaguar input 4 Selection LL EN D fzonel dyall jaguar Figure 2 5 The Jaguar Write dialog box 2 8 Writing Files When you are satisfied with the molecular geometry and the settings that you have made you can either run the job or save the geometry and settings for later use Running jobs is described in the next section To save your input click the Write button at the foot of the Jaguar panel The Jaguar Write dialog box is displayed This dialog box is a file selector with the usual file browsing tools a Filter text box a Directories list a Files list and a Selection text box By default information is displayed in the lists and the filter for the current working directory If you want to write a Jaguar input file containing the geometry and the settings choose Jaguar input from the File Format option menu When you click OK a Jaguar input file is created that is suitable for running a calculation whether from Maestro or from the command line If you want to use the settings for a series of calculations on different molecules you can write a batch scri
539. you want to generate several files To generate output files at the end of each iteration in an optimization set the babelg keyword to the appropriate output extension string Like the babel keyword the babelg keyword can be set more than once to generate files in several formats As files are generated with Babel during Jaguar runs they are immediately copied back to the relevant output directory Files generated from jobs with babel keyword settings have names of the form jobname outext for instance bio spar where jobname is the usual job name and outext is the format keyword which is used as the output extension Files generated from geometry optimizations with babelg settings have names of the form jobnamef outext where is a four digit number corresponding to the iteration number for example 0001 for the first geometry iteration and all letters in the job name are converted to lower case by Babel Note that you can use a babelg keyword setting to write structures generated during an optimization as the optimization proceeds Jaguar 7 0 User Manual 201 Chapter 8 The Jaguar Input File 202 Table 8 31 Output format keywords and file types for babel file format conversions Format Keyword File Type alc Alchemy file bs Ball and Stick file bef MSI BGF file bmin MacroModel file box DOCK 3 5 box file caccrt Cacao Cartesian file cacint Cacao Internal file cache CAChe MolStruct file c3dl Chem3D Cartesia
540. z mann solver which fits the field produced by the solvent dielectric continuum to another set of point charges These charges are passed back to sc which performs a new calculation of the wave function for the molecule in the field produced by the solvent point charges Electrostatic potential fitting is performed on the new wave function the solvent molecule interactions are reevaluated by the Poisson Boltzmann solver and so on until the solvation free energy for the molecule converges For solvation calculations on neutral systems in water whose atoms all have atomic numbers under 19 H Ar by default the program pre evaluates the Lewis dot structure for the mole cule or system and assigns atomic van der Waals radii accordingly For more information on this process see Section 9 6 on page 254 These van der Waals radii are used to form the Jaguar 7 0 User Manual Chapter 5 Output boundary between the solvent dielectric continuum and the solute molecule The Lewis dot structure and van der Waals radii information both appear in the output from the program pre The radii are listed under the heading vdw2 in the table of atomic information below the listing of non default options See Section 8 8 on page 219 which describes the atomic section of the input file if you want information on the other information in this table After the pre output the usual output appears for the first gas phase calculation except that the
541. zmat section Alternatively if the changing coor dinates in the zmat section are set using variables you can leave out the zmat2 and zmat3 sections and specify the second and third geometries by adding zvar2 and zvar3 sections which will be used in combination with the zmat section to define the second and third geom etries See Section 8 3 for details 8 3 The zvar zvar2 and zvar3 Sections The zvar section should contain a list of equations setting the values of any variables in the geometry input in the zmat section in the same units used for the zmat section Here is a sample zvar section Jaguar 7 0 User Manual 159 Chapter 8 The Jaguar Input File 160 amp zvar ycoor 0 753108 zcoor 0 454006 amp For an optimization to constrain freeze all bond lengths or angles set to a particular variable you should add a sign to the end of the zvar section equation setting that variable Similarly to request Hessian refinement of a coordinate whose value is determined by a variable setting in the zvar section just add an asterisk to the end of the equation that sets the variable value in the zvar section For example the zvar section amp zvar ycoor 0 753108 zcoorz0 454006 amp would freeze all ycoor values to 0 753108 during an optimization job Certain types of transition state optimizations require that you enter two or three geometries see Section 4 3 on page 74 for details For these jobs you can spec

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