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Jaguar 5.5 - Stuchebrukhov Group

1. ss 187 188 output from calculations 112 116 probe radius sess 59 188 Solyent CHOICE a eic dtes 59 van der Waals radii for 113 218 221 253 262 Solvation window sss solvent parameters SPARTAN archive files spin multiplicity keyword for oett 169 setting for 33 34 spin populations Mulliken 64 SOM frequency scaling method 66 67 ssh use with MPICH 292 standard functionals dftname values for 174 standard output keywords for 204 205 options for 124 129 structure input see geometry input structure optimizing see geometry optimization structures building eite 9 rotating and translating 14 submission host definition 265 submitting jobs see running jobs S perbloCkS s a o teet d 196 symmetrizing geometry input 37 38 286 symmetry effect on structure sss 286 in IRC calculations 95 186 keywords for 5 ei eceee 169 Option TOr i ciertos 79 output information eee 102 specifying for GAUSSIAN 9x input 144 use of in calculation 37 38 Jaguar 5 5 User Manual synchronous transit quasi Newton methods see QST guided transition state searches T technical SUpport ius
2. 83 141 181 refinement of initial Hessian for 32 33 92 93 165 166 182 psa auem REGE 141 142 334 troubleshooting essss 287 trust radius for 85 86 183 184 188 updating of Hessian during 182 see also transition state optimization geometry SCalls eerte trees 93 94 geometry section Jaguar panel 26 38 geometry translation and rotation of during calculation eret 102 geometry only file reading 286 geometry see geometry input geometry optimization geopt program eeeeeeeeeeeeneentnn 233 QUEPUL iiie resonet 110 112 ghost atoms use in charge fitting to bond Inidpoints es ense ee ee axe eonun 117 Gibbs free energy calculations see thermo chemical properties GPTSEILE 4e rp rrt enti 191 gradient see analytic gradient of energy Grasp program seen 189 grid and RwR information keyword for output Of sessies iranin 205 grid file default sisisi 237 description and format 248 250 specifying in input file 161 Qi ld PORTA cs entrer entire 232 output from ess 103 110 112 grid shell locations keyword for output of 205 faa nla C 84 custom 162 212 for electrostatic potential fitting 62 191 212 grid file cnni 161 information in log file 137 information in output
3. 103 105 keywords for 210 212 253 Selecting DET za niea 50 shells for in grid file 249 250 specified in cutoff file 253 see also grids pseudospectral grids pseudospectral accuracy level se basis set availability keywords for 196 211 212 248 253 ultrafine 1 eiii esiti 78 guess input file section sss 227 Jaguar 5 5 User Manual GVB calculations 56 57 149 155 from HF converged wave function ssss 76 77 199 from HF initial guess 76 from input HF wavefunction 199 generating GAUSSIAN 92 input for 144 GVB data output sese 208 keywords for 170 171 keywords for SCF settings 193 196 output from eee 107 108 131 output OPTIONS oo ee eects 132 pair selection tips 141 printing orbitals restarting troubleshooting gvb input file section GVB pairs choosing from Maestro 56 57 definition riii ttti 150 for GVB LMP2 calculations 58 input file section for 216 217 output information 107 108 selection tips 141 setting from Lewis dot structure 170 171 specifying for GAUSSIAN 92 input generation 144 troubleshooting 286 287 GVB windo
4. SSTT SPET PLUT ESET LY T LLET OCFT O9 TL LEFT VEST 8 TL OLST IL T ISS T 6S9CC 1g 8dd c8 LL I8 8H OS8 hV 6Znd 8LJI LL SO 9L 9H SLIM vLIEL LJH TLT LS eg 96 50 SS TOTT OSC T SETT OIT T GIT TETT PUI PLST OSP T VOV T ISP T 66V TL OTST 8 T COST CLOT ICST LSO T eX vS I S AL cs as IG US OS UI 6vr PO 8r 8V Lv Pd Op QW Sp pr L b OW CP aN IP JZ Op A 6 IS Bela LE ILOT 60 C COLT SIC Orc TOLT T8E T SECUTI LIFT 9 er7 967 T OST TIST CLOT L8S T LOT OOL T 9061 IM O9t d St 9S vt sV ECD Ct D IEJUZ Ot D 6Cc IN 8T OD LTA 9C UN SCHO YTA ETIL TEOS ITIS OTCA 6l 8961 8961 OLOT LYTT LITT 80 C 80 C 80 C Iv 8I D LIS O9I d STS rvI IV el SW CI EN IT 9 L TI 9 L T COLT I 8 T 6r6 1 THOT LE T OCC T N OH 6 0 8N LD 9d ed pI ISTI L6 T 9H C H I SaBADYD PINIA dS jpuuo10q 21171 0422 4 fO uoupqno p ui pasy suo41s8uy U1 LIPDA spoM AIP UDA ZH QPL Jaguar 5 5 User Manual 222 Chapter 9 The Jaguar Input File SSTT 8c PLUT ESET LET LLET OCFT O9 TL LAYI VEST 8 T OLST IST ISS T 68CC tg 8 dd 78ILL IS 9H O8 V Z d S8LMI LL SO 9L eW SLIM YvL L LJH CL I Le ed 96 9D SS TOTT OSES SETT OIT T VOI TETT vcr T PLST OSPI v9 ISP TL 1667 T 90 TL 88 TL COCT CLOT ICS T LO 9X vS I S AL ZS AS IG US OS UI
5. 243 245 246 neighbor ranges for 125 243 245 ordering of sets sese 245 output of number used 204 short range oo 243 245 246 uncontracted suse 244 245 default settings reverting to default atomig file delocalization of LMP2 pairs 172 217 density difference matrix keyword for output of 208 Per Iteration output option 132 RMS of elements in output 105 137 density functional theory DEL eitie 49 54 159 160 customized functional for 53 54 hybrid methods 51 53 keywords for 173 178 210 method options 51 optimization output 109 112 outp t from ere eere 106 standard functionals for 51 53 density matrix convergence criterion TT 84 convergence criterion keyword lof osse deno in DIIS error vector is keyword for output density plotting with plot section 234 236 derta program eei teretes 232 output from seen 109 112 331 Index derTb program etre 232 output from eee 109 112 derivatives of basis functions 129 keyword for list in output 205 DET window terree 49 54 dftname values name strings for con
6. 59 324 processors determining optimum number 298 setting number for a host 266 product geometry for IRC calculations 95 in transition state search 89 specifying in input file 165 specifying in Maestro 90 product installation sss 319 program order specifying 231 234 programs in Jaguar see relevant program name project entries sess ere teneis 7 including excluding and fixing 8 Project Facility introduction to T Project Table panel sss 8 juu P a properties keywords for sss 188 191 Options for eite tsetecienise 60 69 Properties window 60 64 electron density sess 63 ESP charge fitting 60 62 Mulliken population analysis 64 multipole moments es 62 output from eee 116 121 polarizability and hyperpolarizability 62 63 pseudospectral method 147 149 publications citing Jaguar in 3 Q QST guided transition state searches 89 90 additional structures for 165 166 keyword FOr etiem 180 LMP delocalization for 173 218 quadratic energy error keyw
7. 212 213 214 iqmedium 212 213 214 Mqst ues Iqufime nei 212 213 214 346 ECMA cisci on RED PRIUS ircmode ircmxcyc ircstep yn M iteray ouo dr poe R itradj itrcut jac lastWyv A EPOR Icoarse Idips iustis Di ethan asi devespasdesrzane lewdot ceto 170 171 172 lewstr 170 171 187 262 Jue M Imedium loclmp2c loclmp2v locpostc LOCDOSEY 5 oh Dn aas lufine ianen Jaguar 5 5 User Manual M MASS e 220 massav 169 maxciit jl 79 maxdiis multip e OE RERAA 169 220 ImXpage uncta ote sae exi Rods 213 nq e 213 qa dee ES 213 incip 213 N hlgcnr dem 213 nd 213 ndford Xl ioni pP 210 ndferdX2 eric tecittdentes 210 Iq EN 213 needgwd i ioi ie metddesies 181 newcon nhesref nmder Ping 195 III 196 HOPAS E HR 180 nodis oce 181 noopta iz nooptr nooptt HOPS ii diutius ed istius iritice Geos BOSUpeE eec rere eati en ea 196 noupdaft 5 irren 195 li 235 nrestart 49 nroot 179 ntemp orientar poten ia 192 DUmd aiio disp DES 71 193 O OFIglI 25a cnet dado iia esu ds 235 Jaguar 5 5 User Manual Keyword Index P p rind 45 5 cep RHEIN 180 184 plot mt ue metet dee pena 216 plotres onr HER ERU roten 215 DEOSS Loo ett AE 192
8. Keyword Value Description basis n no or Use no basis functions on atom none basis name Use basis functions from specified basis set on atom grid n no or Do not include any grid points on atom none only Include grid points on atom but no basis functions dealias ing functions or nuclear charge daf n no or Do not include any dealiasing functions on atom none only Include dealiasing functions on atom but no basis func tions grid points or nuclear charge charge n no or Treat atom as a counterpoise atom do not include nucleus none or electrons for atom only Include nuclear charge on atom but no basis functions grid points or dealiasing functions 9 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 fragment be treated as dummy atoms or counterpoise atoms or used as the only atoms for which numerical frequencies will be calculated 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 frag ment 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 make the keyword setting icpfrag fragno in the gen section of the input file where fragno i
9. 100 for each atom sees 102 intermediate sese 101 RFO level shifting keyword for 182 chosts file use with MPICH 292 RODFT see restricted open shell wave functions ROHF see restricted open shell wave functions row Project Table sss 7 Run window sss 25 38 40 263 running jobs from Maestro 25 38 46 from the command line 269 271 individual sss 38 40 multiple 40 44 on a remote host sees 270 selecting a Jaguar version 271 troubleshooting 281 286 341 Index OWI prtOSTai tester irony 232 execution sequence 109 110 S sample calculation 23 26 Save window ccccccssccesseeesseeessees 44 45 162 scaling frequencies cece 66 67 Keywords for see 192 scanning geometries 93 94 SCF energy Output esee 104 SCF iterations keywords for eee 207 maximum number of T1 139 SCF level shift uec dre 78 SCF method keywords 193 SCE propras arie RR 232 GVB calculations 108 output from 103 105 107 108 110 112 115 131 132 solvation calculations S
10. 46 47 332 effective core potentials ECPs basis sets for 72 14 in atomic guess file 243 in basis set file 239 241 efields input file section 229 eigenvector following in transition state optimizations keywords for sss 182 183 option setting eese 91 use in Hessian refinement 92 elden program eee 232 electric field for polarizability calculations input file section for 229 keyword for oot 191 electron count information in output 104 electron density evaluating on a grid 63 keywords for 189 191 211 output from calculation 119 electrostatic potential in resp file sse 207 output on a grid sess 191 electrostatic potential fitting constraining to reproduce multipole moments cesses 61 142 for LMP2 wavefunctions 61 for solvation calculations 58 112 113 PTI FOL ient pro rere eins 62 keywords for control of 188 keywords for grid 191 212 output from see 117 118 recalculating multipole moments from 62 RMS error in output eee 117 setting options fOr eee 60 energy components keywor
11. BHandHLYP Exchange 50 exact HF exchange 50 Slater local exchange func tional 29 correlation Lee Yang Parr local and nonlocal functionals 33 B97 1 Reparametrization of Becke s 1997 hybrid functional 36 by Hamprecht Cohen Tozer and Handy 39 52 Keyword dftname bp86 vwn5 in gen section of input file Keyword dftname pwp91 in gen section of input file Keyword dftname hcth407 in gen section of input file Keyword dftname pbe in gen section of input file Keyword dftname b3lyp in gen section of input file Keyword dftname b3pw91 in gen section of input file Keyword dftname b3p86 in gen section of input file Keyword dftname bhandh in gen section of input file Keyword dftname bhandhlyp in gen section of input file Keyword dftname b97 1 in gen section of input file Jaguar 5 5 User Manual Chapter 4 Options B982 Becke s 1998 hybrid functional including the Laplacian of the density and kinetic energy density terms as well as gradient terms 37 e SB98 Schmider and Becke reparametrization of Becke s 1998 functional 38 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 instead of idft to specify the functional The names are case insensitive 4 1 3 Custom Functionals The four menus below the DFT Model option menu provide information on which func tionals are curre
12. 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 Continue to the next job if a job step fails The default is to stop execution of the batch script and exit Purge the job record for each job after it finishes Exit from the batch script 276 Jaguar 5 5 User Manual Chapter 11 Running Jobs 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 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 speci fied 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 If the file new name in already exists it is overwritten 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
13. DFT Density functional theory calculations Local MP2 Local Mgller Plesset second order perturbation theory calculations GVB Generalized valence bond calculations Optimization Geometry optimization and forces Solvation Solvation energy calculations Properties Multipole moments and charge fitting and hyperpolarizability proper ties Frequencies Vibrational frequencies IR intensities and thermochemical properties Basis Set Basis set options Methods Initial guess convergence orbital localization and various technical settings Surfaces Generate plotting data for visualization of surfaces in Maestro In addition you can perform pK calculations and J2 theory calculations using a built in batch script Optimizations are described in Chapter 5 and the other GUI options are described in Chapter 3 and Chapter 6 The footnotes in this chapter indicate the Jaguar input file keywords and sections that correspond to settings made in the GUI 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 3 9 3 on page 46 4 1 Density Functional Theory DFT Settings The density functional theory module in Jaguar allows you to employ a variety of func tionals to describe exchange and correlation for either open or closed shell systems The theory
14. 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 calculates terms dependent on geometry e g nuclear repulsion energy onee Calculates one electron integrals and effective core potential ECP contribu tion to one electron Hamiltonian when relevant hfig Calculates Hartree Fock initial guess probe Insures 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 fitting Mulliken populations lmp2dip Calculates dipole moments for LMP2 wavefunctions 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 Mgller Plesset perturbation theory calculation cis Performs CI singles calculation derla Calculate analytic one and two electron first derivatives derib lmp2der Calculate analytic one and two electron first derivative terms for LMP2 lmp2gda wavefunctions lmp2gdb nude Calculates numerical second deriv
15. initial wavefunction generated automatically from atomic wavefunctions Next a table lists the number of orbitals and of occupied orbitals in each shell having each irre ducible representation 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 wavefunction generated automatically from atomic wavefunctions Irreducible Total no No of occupied orbitals representation orbitals Shell 1 Shell 2 Al 12 3 A2 2 0 B1 4 1 B2 7 all Orbital occupation shell 1 000 end of program hfig The probe program which follows hfig and insures orthogonalization has no signifi cant 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 10 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 5 number of beta electrons
16. 0 000 beta y z z 0 000 beta z x x 0 435 beta z y 0 404 Mu Nn z 0 000 sum beta x 0 000 sum beta y 0 000 sum beta z 9 367 beta 5 620 118 Jaguar 5 5 User Manual Chapter 6 Output second hyperpolarizability in AU gamma x x x x 7 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 amp and Ao are reported as alpha and Dalpha defined as follows O Apy O 3 2 2 2 AQ E o 0 0 6 Oyy For the first hyperpolarizability three sums are reported which are defined by the following expression Yp Bary Bayy Bazz where q can be x y or z The average hyperpolarizability D is defined by B ES tu Ep up where p is the dipole moment The average second hyperpolarizability y is defined by Y 22 2 oe P q where p and q run over the three coordinates x y and z 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 t
17. 184 191 193 SCAN ecce anena 66 67 192 visualizing in Maestro 67 visualizing with Molden 66 viri l fatio serere 204 virtual orbitals sess 105 208 number printed sss 134 W wave function type 74 workflow project based 7 Workspace descripti Olssen nsen 7 including excluding and fixing entries 8 Scratch entry sicvivesecssistersassealictssisesserseress 9 X 343 Index Z zero point energies see thermochemical prop erties zmat input file section sess 164 zmat2 input file section 164 zmat3 input file section 164 344 Z matrix format 27 29 32 164 166 dummy atoms in eee 31 variables in ss 31 32 166 zvar input file section 0 eee eee eee 166 zvar2 input file section sssse 166 zvar3 input file section sssss 166 Jaguar 5 5 User Manual Keyword Index Numerics Msi DNE IEEE EE 220 201 204 201 204 193 225 C ura w desee Charge 4b retro EL t E RR COV ou covfac i CUL c ee aT HUM D nb EN 225 dceoarse eo e optet i tr ce esie bends 212 dc nv i usenescieieeieen 183 190 193 194 G gcharge eee 191 212 253 QCOATSE M 212 253 gcon
18. 2 4991970000000 0 0000000000000 1 2495990000000 2 1643680000000 2495990000000 2 1643680000000 0000000000000 2177610000000 2177610000000 0000000000000 2177610000000 2177610000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 0000000000000 I NNOA 0O 0 cooooooooooo Figure 3 11 The Edit Job window You do not need to use the Edit Job window to do anything described in Chapter 3 through Chapter 6 However if you prefer to set up jobs with keywords or if you want to use any options described in Chapter 9 that are not set by the GUI the Edit Job window provides you with a convenient way to do so To use keywords to set options that can be set by the GUI refer to the footnotes in Chapter 4 and Chapter 6 to find out which keyword settings are appropriate If you make and save a setting in the Edit Job window that corresponds to something shown by the GUI the GUI selection shows the change If you select a keyword by double clicking on it or dragging over it a brief description is displayed at the bottom of the window if there is information available for the keyword To see a fuller description open the online help by clicking Help If the input file contains unrecognized input a warning is displayed that the keyword is unrecognized when you run the job or save the input f
19. 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 refine ment 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 describes the internal coordinates and optimization variables as stretches bends or torsions and indicates 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 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
20. S del m hacia MR 192 SCODY lico osten ditor aa rers cc dat 188 SIGHS c Soon on MUNI 194 T AMP soie dev irte tete int 192 impstp i25 necne btts 192 tradimn concor HERES A 184 AdE ueri ben 184 EMS uoo der IRE EE ER OAS 184 eok cau eu tes 184 V VOW xotensditen tard avs 220 VAW issu d anm On e 220 NShift iicet np 178 194 195 W WISDC iode Ond GEHE IE 190 191 X xad iot inox ere e Rd pde 215 xcorl1 xcorl4 177 178 xcornl1 xcornl9 177 178 Xexll 5 secco 177 178 xexl9 unc gi t RII 177 178 xexnl1 xexnl9 177 178 ji mx 177 178 xmaxad 4 2 nere soe 215 xminadj iecit 215 347 Keyword Index Y Vad iiisotuse ctio irte aua tive ycorl1 ycorl4 ycornli1 ycornl9 yell io ote m Vex anan ena yexnl1 yexnl9 sess WHE m 348 ymax d io eon bn D dod bns 215 ymin adj rr Dai HERES 215 Z ZAA ocio dob n UR Hb zmaxadj zminadj Jaguar 5 5 User Manual 120 West 45th Street 1500 SW First Avenue 3655 Nobel Drive Dynamostrafe 13 32nd Floor Suite 1180 Suite 550 68165 Mannheim New York NY 10036 Portland OR 97201 San Diego CA 92122 Germany SCHR DINGER
21. Schlegel H B Theor Chim Acta 1984 66 333 CRC Handbook of Chemistry 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 1074 A cm where r is the solvent probe radius in Angstroms m is the TP MM mass obtained by dividing the molecular weight given in ref 52 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 52 Finding the actual A vould 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 5 894 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 II 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 M
22. Table 11 8 The jaguar batch Command Line Options Option Description C Create input files but don t run the batch job 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 generated 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 jobsteps 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 If you run remote batch jobs you should ensure that the input and output directories are on a disk system that is available to both the submission and the calculation host such as a cross mounted disk or an NFS file system 280 Jaguar 5 5 User Manual Chapter 12 Troubleshooting Naturally we hope that you will never need to use this chapter However if you have prob lems using Jaguar you may find
23. as described below the multipole moments are also calculated from these point charges for comparison 4 6 3 Polarizability and Hyperpolarizability You can calculate polarizabilities and first hyperpolarizabilities by making the appropriate choice from the Polarizability Hyperpolarizability options menu To calculate second hyper polarizabilities you must set ipolar 2 in the gen section of the input file 38 Keyword gcharge 1 in gen section of input file 39 Keyword gcharge 2 in gen section of input file 40 Keyword wispc in gen section of input file 41 Keyword ldips 2 3 4 or 5 in gen section of input file 62 Jaguar 5 5 User Manual Chapter 4 Options The coupled perturbed HF option calculates both polarizability and hyperpolarizability using coupled perturbed Hartree Fock CPHF techniques In general this option is supe rior to the finite field option but the CPHF option can be used only with closed shell and unrestricted open shell wavefunctions and with basis sets that do not use effective core potentials In Jaguar the basis sets with effective core potentials are CSDZ and those with names beginning with LA See Section 4 8 on page 70 for information on basis sets The finite field option 17 uses a 5 point finite difference method which employs the results from 13 SCF calculations one with no field one with an electric field of E where E is 0 024 au by default in the x direction
24. smearing 127 2 Use pseudo fractional occupation number pFON method for ther mal smearing 127 fdtemp 10000 Initial temperature in K for thermal smearing 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 One of the most important keywords in controlling the SCF is iacscf This keyword should be employed when the SCF fails to converge under the default conditions 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 related mole cules while iacscf 3 was effective for graphitic systems Energies obtained with iacscf 2 can be directly compared to energies obtained without using iacscf Energies obtained using other values of iacscf are not comparable because they use different grids or cutoffs Another method for controlling SCF convergence is thermal smearing 127 Thermal smearing is a method for improving 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 kT Two methods for determining the occupation numbers have been implem
25. 1 2 ethanedithiol 9 1 9 1 0 0 SULFONAMIDES N chlorotolylsulfonamide 4 6 4 5 0 1 dichlorphenamide 7 5 7 4 0 1 mafenide 9 3 8 5 0 8 methanesulfonamide 10 2 10 5 0 3 quinethazone 9 3 9 3 0 0 saccharin 3 1 1 6 1 5 sulfamethizole 4 3 5 4 1 1 sulfaperin 6 9 6 8 0 1 sulfacetamide 6 1 5 4 0 7 Jaguar 5 5 User Manual 309 Chapter 14 The pKa Prediction Module Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group MOLECULE pKa calc pKa exp Deviation sulfadiazine 6 4 6 5 0 1 sulfadimethoxine 6 9 6 0 0 9 sulfamethazine 7 2 7 4 0 2 sulfanylamide 10 9 10 4 0 5 sulfapyridine 7 7 8 4 0 7 sulfaquinoxaline 6 0 5 5 0 5 sulthiame 10 3 10 0 0 3 HYDROXAMIC ACIDS formohydroxamic 8 1 8 7 0 6 acetohydroxamic 8 4 8 7 0 3 benzohydroxamic 8 4 8 8 0 4 salicylhydroxamic 8 4 T5 0 9 2 aminobenzohydroxamic 9 0 9 0 0 0 2 chlorobenzohydroxamic 8 3 7 8 0 5 2 fluorobenzohydroxamic 8 2 8 0 0 2 2 nitrobenzohydroxamic 8 5 7 0 1 5 3 nitrobenzohydroxamic 8 2 8 4 0 2 4 aminobenzohydroxamic 8 9 9 4 0 5 4 chlorobenzohydroxamic 8 4 8 7 0 3 4 fluorobenzohydroxamic 8 4 8 8 0 4 4 nitrobenzohydroxamic 8 2 8 3 0 1 4 hydroxybenzohydroxamic 8 6 8 9 0 3 IMIDES fluorouracil 8 6 8 0 0 6 methylthiouracil dad 8 2 0 5 phenytoin 7 1 8 3 0 6 3 3 methylphenylglutarimide 10 4 9 2 1 2 310 Jaguar 5 5 User Manual Chapter 14 The pKa Prediction Module Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional
26. 195 obtaining i o information for 125 pseudospectral assembly of 148 149 excited state calculations using CIS keywords for se 179 setting options for oo eee 75 executable directory 102 269 selecting with jaguar run 271 execution path see 231 234 F field electric input file section for 229 file Vo directory noce trenes 18 file names wa 39 45 file output keywords sss 206 file output options 129 131 GAMESS input file 207 GAUSSIAN 92 basis set gbs file 145 GAUSSIAN 92 input g92 file 144 keywords for e 206 XYZhleicdehoh fan iut 130 Jaguar 5 5 User Manual Index first shell correction factor for solvation keywotd fot eire rete 187 Fock matrix in DIIS error vector 105 137 keyword for updating 195 keywords for output of 205 208 new estimate from DIIS scheme sss 105 132 137 Per Iteration output options 132 pseudospectral assembly of 147 149 updating errare 104 137 forces analytic availability 83 calculating only sess 83 keywords for s 180 184 numerical availability 83 numer
27. Beachy M D Wang L Friesner R A Parallel Pseudospectral Electronic Structure I Hartree Fock Calculations J Comput Chem 1998 19 1017 Beachy M D Chasman D Murphy R B Friesner R A Parallel Pseudospec tral Electronic Structure II Localized M ller 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 5 5 User Manual Index A About button eessssseeeeee 47 263 accuracy level we 78 84 input keyword for 195 accurate enerpies etti rente 81 acidic site designating for pK calculations ees 315 AIMPAC wfn file input keyword for 207 all analytic calculation 78 input keyword for 195 o tput IrOm oet eet mes 123 analytic corrections see 78 keywor
28. Cc Oc O OQ OQ OCOONNN OO SCORRRO OONNNO 10 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 248 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files 10 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 Lead zeros 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 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 de fault grid is actuall
29. Fa Cy FC s k Here F is the Fock matrix S is the overlap matrix and T is the residual matrix defined by this equation The exchange matrix K is restricted to the dimensions of the virtual space corresponding 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 equa tion Pq chy cfs D a E E E E7 where and are the matrix elements F and F in the localized molecular orbital basis and e and e 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 energy domecton E 2 from the equations ij EO Y K4 21a i2j Jaguar 5 5 User Manual 157 Chapter 8 Theory Gi 1 8 46 2C 21b where the bracket in Equation 21a denotes a trace and 8 is 1 if i j and 0 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 20 of the work Jaguar performs localized MP2 calculations using pseudospectral methods evaluating integrals over grid points in physical space in a manner similar to that described for HF and GVB calculations in Section 8 1 on page 147 and Section 8 2 on page 149 The two electron exchange integrals needed for Equation 21a are eva
30. 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 hybrid ization type information should end with a blank line 10 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 Jaguar s 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 contra diction If no such matching description exists in the Lewis file the atom is assigned the default radius for that element 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 wavefunctions or RADII TYPE 02 for information for LMP2 wavefunctions After that each atom t
31. Jaguar runs the program pbf once more to get the solvation related gradient This pbf output does not contain the usual solvent accessible surface area and cavity energy terms The programs deria 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 geom etry optimization convergence criteria are reached The convergence criteria for optimiza tions 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 solvated structure that was optimized in solution 6 3 0 Properties If you make any non default selections from the Properties window the program ch runs and writes the results to the output file after the SCF iterations if any When multipole moments are calculated the x y and z components of the dipole moment and the total magnitude of the dipole moment u are reported in Debye followed by infor mation on any requested higher order moments and the corresponding traceless higher order moment tensors For example
32. Table 9 17 Integer Keywords for Geometry and Transition State Optimizations Cont d Keyword Value Description 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 iaccg 2 Use default convergence criteria shown in Table 9 19 3 Perform quicker coarser calculation by multiplying convergence criteria shown in Table 9 19 by 5 4 Solution phase criteria a factor of 3 times the criteria shown in Table 9 19 nogdiis 0 Use GDIIS method Geometry optimization by Direct Inversion in the Iterative Subspace 117 to get new geometry 1 Don t use GDIIS method ilagr 0 Apply constraints by zeroing gradient along frozen coordinates pre v2 3 method not recommended 1 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 specifical
33. 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 The atoms are indicated with the atom labels assigned in the geometry input When the Optimize geometry option in the Geometry Optimization window has been turned on the bond lengths and angles standard output option is turned on automatically For geometry optimizations bond lengths and angles are also listed with the output from the program geopt 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 daf file See Section 10 3 on page 243 for more information All of the diagonal entries are 0 indi cating that the row atom and the column atom for the matrix element are the same atom Keyword ip6 2 in gen section of input file Keyword ip26 2 in gen section of input file Keyword ip25 2 in gen section of input file Keyword ip11 2 in gen section of input file Keyword i
34. buvKy 12 v Each orbital s Fock operator thus depends on the other orbitals Coulomb and exchange operators 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 YP in the basis of the two natural orbitals in pair p as described by these equations Y c CE 13a 1 Nub o p i E Ype pg 7 P pg pg 2 pg pet gt Cog 24 ag pg 7 Kag pg q p N vb 2 t Y Cou 27 qu pg 7 K qu pg 13b q p 1 MP p 1 Y ju pu P pu put 27 pu pu t gt Cas 27 ag pu Kag pu q p N vb 2 A Y Cau 27 qu pu Kqu pu 13c q p p Sou ral Ypg pu Y pu pe 5 pg pu 13d 152 Jaguar 5 5 User Manual Chapter 8 Theory In practice since the CI coefficients are mutually interdependent they are determined using a self consistent iterative procedure 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 accord ingly in basically the same manner used for the usual HF treatment The revised orbitals and CI coefficients are then used in the next SCF i
35. comma of all basis sets for which the atomic calculations listed immediately after that line apply The basis set names are listed in Table 4 3 on page 71 and Table 4 4 on page 73 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 basis 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 indi cates 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
36. constraints on bond lengths or angles for geometries containing second bond angles All additional lines of the Z matrix should have the same form as the fourth line The complete Z matrix for the example molecule the 150 conformation of glycine is N1 c2 N1 1 4589 c3 C2 54 5203 N1 115 32 04 C3 1 2036 C2 126 28 N1 150 0 05 C3 1 3669 C2 111 39 N1 31 8 H6 N1 1 0008 C20 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 73 H10 05 0 9656 C3 111 63 C2 178 2 3 2 6 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 easie
37. convergence criteria These criteria are all affected by the Convergence criteria choices default or loose the loose criteria are all five times larger than the default criteria For optimizations in solution the default 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 6 Keyword dconv in gen section of input file 7 Keyword iaccg 2 in gen section of input file 8 Keyword iaccg 3 in gen section of input file 84 Jaguar 5 5 User Manual Chapter 5 Optimizations and Scans See Section 9 5 9 on page 179 if you want more details on the geometry optimization convergence criteria or information on how to edit the input file to set them directly 5 1 3 The Initial Hessian To perform an optimization Jaguar first needs to read or generate an initial Hessian second derivative matrix or force constant matrix You can provide Jaguar with a Hessian in the hess section of an input file as described in Section 9 9 on page 226 For instance if you restart a geometry optimization from a previous job as described in Section 7 2 on page 142 Jaguar automatically uses the Hessian provided in your input file If your input file does not contain a Hessian you can use the Initial Hessian option menu in the Optimization window to specify what
38. 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 92 files or BIOGRAF hes files AII 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 of these rows containing five or fewer matrix elements starts with an integer which is read first this integer is not used in the program but can be used to label the matrix elements for convenience in looking over the file When the relevant matrix elements from that entire five column block have been read in the next block is read in in the same way until all of the matrix elements for the bottom triangular half of the matrix have been entered 226 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File For example in
39. general description and format 161 164 in jaguar run command 269 271 keywords ete tnter mets 168 213 Imp2 keywords sss 172 MAING 270 POAC Gs se sordium 34 35 reading in Maestro 34 35 286 we 142 143 PESAT seoti sin kasiis saving with Save window 44 45 section delineators 163 spacing characters cece 162 summary of sections ses 163 input file sections ATOMIC iin ie eee e Reds 218 226 CONNEC 166 168 COOEG Goethes 166 168 o nM 231 hields ana edet tire 229 POM 168 213 PUES aiiis eiie a eter 227 228 PVD ssasisvisesaistiensiedivtiassattessiteveiene 216 217 hr A 230 hr M 226 227 Imp2 5s atte ti 172 217 218 ilo M N 236 OLDMAN eierens 230 231 paths istas dei 231 234 plot eet rede 234 236 powitehi iui etr erra 229 164 165 AC 164 zvar Zvar2 zvar cccecccessscccessseeeees 166 input of molecular structure see geometry in put installation directory 281 282 integrals one electron 102 336 integrals two electron contributions to energy 107 131 number and type computed 78 internal coordinates in optimization keyword for 180 specifying with connect section 166 168
40. one with a field of E in the x direction four others with fields of E and E in the y and z directions and six others using fields of aE and aE in the x y and z directions where a is a constant determined automatically Both hyperpolarizability methods are run without using molecular symmetry Also for any polarizability calculation the energy convergence criterion which is set in the Methods window is set by default to 1 0 x 10 If you want to change the electric field used for the finite field calculation or to use other finite field methods to calculate the polarizability and hyperpolarizability see Section 9 5 12 on page 188 for information on editing the input file appropriately 4 6 4 Electron Density The electron density for the final wavefunction can be evaluated on a set of grid points The Cartesian coordinates of these grid points and the electron density in au respectively for each grid point are written to the file jobname chdens where jobname in is the input file for the Jaguar job If you select rectangular for the electron density calculation the grid used is rectangular with spacing in Angstroms determined by the density grid spacing set immediately below For spherical the default choice the electron density is evaluated on the ultrafine grid used by the pseudospectral method We recommend using the spherical grid for quan titative results although the rectangular grid is sometimes useful for d
41. rather than just the basis set name within the g92 file This option is useful for specifying basis sets which are included in Jaguar but not in GAUSSIAN 9x Setting ip160 to 4 allows you to include both the initial guess and the basis set in the g92 file 7 3 2 Getting Basis Sets or Orbitals for GAUSSIAN 9x The preceding subsection describes how to generate basis sets or orbitals for a GAUSSIAN 9x input file You can also output a basis set in the format used by GAUSSIAN 9x by turning on the Gaussian 92 basis set gbs option in the File Output window The output is written to a file with the extension gbs You can write orbitals from Jaguar in the format used by GAUSSIAN Ox for its guess cards option by choosing to print the appropriate orbitals from the Orbital Output window which is described in Section 6 7 on page 133 You must choose the f19 15 or f8 5 format from the How option menu 7 3 3 Using GAUSSIAN 9x Files as Jaguar Input GAUSSIAN 9x input files can be read in the GUI which reads the molecular geometry from them and also turns symmetry off for the calculation or turns on electrostatic potential fitting to atomic centers if the GAUSSIAN 9x input file requests either of those options Any other Jaguar settings take on their default values For information on scanning in GAUS SIAN Ox input files as Jaguar input see Section 3 4 on page 34 Jaguar 5 5 User Manual 145 Chapter 7 Tips and Suggestions 146 Jaguar 5 5 U
42. specifying with coord section 166 168 intrinsic reaction coordinate IRC calculations niisiis 95 185 IR intensities see infrared intensities ira IOgTAIm csset 232 DED program terret ten 232 ISOLOPES weiss 218 220 keyword for gen section 169 iterations maximum number geometry optimization 83 141 181 SCE chon eines 77 139 195 J J2 theory calculations 81 jaguar command sese 282 jaguar command s 266 275 jaguar babel 272 275 jaguar batch 275 280 jaguar help ulioseheesines 267 jaguar jobs netos 267 Jaguar JEkwoll 3 emen 211 jaguar machid 267 jaguar platform 267 jaguar results 97 102 Jaguar T lhioseeeeierioserens 269 271 jaguar Sysreq ene 267 Jaguar copyright information 102 Jaguar data directory 237 Jaguar files nee 237 Jaguar programs see 232 JAGUAR SCRATCH environment variable 266 JAGUAR SCRIPTS environment variable 41 jexec program ssseeeeeeeeee 232 job directory local 39 45 39 45 102 266 270 DP 46 K keywords atomic Iri ss iseecehritettes 169 dealiasing function is 210 file o tput cases esie 206 Jaguar 5 5 User Manual frequency related properties 1
43. table are from ref 61 and are optimized for the best agreement with experiment for the frequencies themselves Ref 61 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 Table 4 2 Recommended Frequency Scale Factors for Various Combinations of SCF Method and Basis Set taken from Ref 61 SCF Method Basis Set Scale Factor HF 3 21G 0 9085 HF 6 31G 0 8953 HF 6 314 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 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 4 7 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 calculations 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 anima tion You can switch modes an
44. transition state guess and product structures if you have provided all three of these structures in your input If you know the 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 setting Search along to user selected eigenvector and specifying the eigenvector number in the text box marked Selected eigenvector You can identify the eigenvector number by running one geometry optimization iteration see Section 5 1 1 on page 83 for information and examining the output summary of the Hessian eigenvectors which indi cates the dominant internal coordinates and their coefficients for each eigenvector 5 3 5 Eigenvector Following The setting for Eigenvector following determines whether a minimization will follow a new eigenvector each iteration the default behavior with eigenvector following off or whether the transition state optimizer will follow the eigenvector that most closely corre lates with the one chosen the previous iteration 25 Keyword itrvec 0 in gen section of input file 26 Keyword itrvec 1 in gen section of input file 27 Keyword itrvec 2 in gen section of input file 28 Keyword itrvec 5 in gen section of input file 29 Keyword itrvec gt 0 in gen section of input file 30 Keyword itrvec gt 0 in gen section of input file where itrvec is the relevant eigenvector num ber for the
45. 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 256 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files The format of the hybridization type information is very similar to that of the bonding type information The first line of this information for HE 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 information 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 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 hydro gens bonded to sp carbons by listing carbon s
46. x a zO 3 20 Eu OoOo00U0 1U oO OW OW 2 x N BO m CI YO AT c CP Oma aS a 2 3 a Ss E e E e ex 00 0 e x NOB I SCORPRRO hI OS eS r Ose dlc O O O WW WW oOoOWNY WwW OO OW OW x M ID an ea S OcOornmuuc OOo o0o00o0 OO Oooo oS OOO Oc oO Cx BM M NG COrRRRO Oo Oo a co 2 2 cc gt Bay uooo o OOO WWW oOoOW NY WwW OO OW OW OCOONNOOO ec cm uuo Cc mmo Cc c ocu cec oO ooo OCONNN OO CORRRO OOO oou oo Oo ca o COO OW WW WW Oco00U0 1 1U OO OW OW oS SIO IN a O t U co c E aao 2a co oO Sm SS Oso Oo oco o Go BR GO SCORRRO OCOONNNO 2 10 2 He 0 071497 0 145957 0 297964 0 608279 1 241774 2 535023 5 175131 10 564786 21 567514 1 100000 Jaguar 5 5 User Manual 247 Chapter 10 Other Jaguar Files e O0 UO om O OOOO OW Oo O0 IW oO OoOoO0oU0o0octu O ONV UV GOO O Cc HP A T O o O O OOo o o e oo amp oo oc cuo O O V u v OO oOompmpBnmp bHmbpPo oO OO c Coo O cC O0 O OC C O Cc C OO Uu oO oO0U0 Uu C C O Ww Ou O cC b No o O O S A A co cO O GOG GOG O O O o0 co O oo Oo O cz C cC NM bk N SG CORRRO oo O O cO ooo oo amp OOO WW WwW QOO Ur TN WwW oo Oo uoc u OO W u GO GO cOoHnmuuc O O O OG OG OO O O G O oc ao oo O OONNN OC SCORRRO oo OOo O c cO OO oO OOO WWW CO oO U0 TN YW c UO O 0 O uw Cc C NN Oo oc oorno c OOO OG Cc C O O O O oo o OO oO OCOONNNO SCORRRO c c O O OO Cc c ca QO OQ O OOO WW WW oOoOoOWN YN WwW cO Uo amp OONNOOO oorUW WU c Cc Cc OO OQ O0 oq C O O O
47. zmat3 section of input file 24 Keyword qstinit in gen section of input file 90 Jaguar 5 5 User Manual Chapter 5 Optimizations and Scans 5 3 4 Searching Along a Particular Path or Eigenvector If you are using the standard non QST guided optimization transition state optimization method you can use the Search along option menu to specify a path for the optimizer to follow or an eigenvector for it to minimize each iteration the lowest Hessian eigenvector the default the lowest non torsional mode the lowest bond stretch mode the reac tant product path or a user selected eigenvector 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 eigenvector found for each iteration The lowest non torsional mode and lowest bond stretch mode options can be useful for steering the optimizer to a particular type of transi tion state for instance for a study of a bond breaking reaction you can avoid converging to a torsional transition state by choosing lowest bond stretch mode The reactant product path option causes the optimizer to follow the Hessian eigenvector that is most similar to the direction of the linear path between the reactant and product structures if you have provided these two structures but no transition state guess in your input or the tangent of the circular curve between the reactant
48. 181 in solution ssesss 58 60 180 initial Hessian 32 33 85 93 165 181 182 keywords erret 179 183 level shifting of Hessian 182 limiting step size for maximum iterations refinement of initial Hessian 32 33 92 93 165 166 182 Jaguar 5 5 User Manual Index search method sss 89 trust radius 85 86 183 184 updating of Hessian 182 trial wave function see Initial guess troubleshooting esses 281 287 trust radius for optimizations 85 86 183 188 two electron integrals number of 78 U UDFT see unrestricted wave functions UHF see unrestricted wave functions undoing a Maestro operation 17 unrestricted wavefunctions keyword for eese 194 option for 74 user name setting for different hosts 265 V van der Waals radii 62 221 for solvation calculations 187 input file sections for 218 221 listed in output sess 113 setting from Lewis file data 258 van der Waals surface cece 62 variables in geometry input 28 29 31 32 87 88 166 versions of Jaguar listing 269 vibrational frequencies 65 66 keywords for
49. 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 54 7406 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 Burke K Ernzerhof M Phys Rev Lett 1996 77 3865 Phys Rev Lett Erratum 1997 78 1386 Meller C Plesset M S Phys Rev 1934 46 618 Jaguar 5 5 User Manual 323 References 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 324 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 III J Chem Phys 1987 86 862 Fischer T H Alml f J J Phys Chem 1992 96 9768
50. 275721 1 000000 0 275721 Oo 9 S 2 1 013762 0 814208 1 000000 0 814208 Oo 10 X 3 15 539616 3 116944 1 000000 3 116944 Y 4 1 000000 3 116944 Z 5 1 000000 3 116944 Oo 11 X 3 3 599934 2 401438 1 000000 2 401438 Y 4 1 000000 2 401438 Z 5 1 000000 2 401438 O 12 AX 3 1 013762 1 054360 1 000000 1 054360 Y 4 1 000000 1 054360 Z 5 1 000000 1 054360 Oo T3 3S 6 0 270006 0 266956 1 000000 0 266956 O 14 X v 0 270006 0 277432 1 000000 0 277432 128 Jaguar 5 5 User Manual Chapter 6 Output Y 8 1 000000 0 277432 Z 9 1 000000 0 277432 Oo 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 1 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 E NE S 0 640122 0 415051 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 1 000000 1 605761 Z 20 1 000000 1 605761 H2 1 5 21 18 731137 0 214935 1 000000 0 214935 H2 2 9 2T 2 825394 0 364571 1 000000 0 364571 H2 3 55 21L 0 640122 0 415051 1 000000 0 415051 H2 4 S 22 0 161278 0 181381 1 000000 0 181381 H2 5 x 23 1 100000 1 605761 1 000000 1 605761 Y 24 1 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 Gaussian function list derivatives By tu
51. 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 informa tion about both pseudospectral and DFT grids for a job by setting ip23 2 in the input file Table 9 36 shows the types of grids that can be specified for portions of the calculation that do not involve density functional theory Generally these grid types are used for pseudo spectral SCF iterations or for charge fitting The grid related keywords and their allowed and default values are given in Table 9 37 where name corresponds to one of the grid types listed in Table 9 36 As an example gmedium z2 indicates that the medium grid to be used for the calculation is the second one listed in the grid file while geldens 3 indicates that an electron density calcu lation should use a cubic grid Table 9 36 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 Imp2der Grid used for LMP2 gradient calculations charge Grid used for charge fitting eldens Used for electron density calc
52. 5 The pern SEObOofi eieo etit eine eet tee eet terree eere deter tree b cebey ee eie 168 9 5 1 Geometry Input Keywords eese 168 9 5 2 Molecular State Keywords Charge and Multiplicity 169 9 5 3 Atomic Mass Keyword nennen 169 9 5 4 Symmetry Related Keywords eee 169 9 5 5 GVB and Lewis Dot Structure Keywords ees 170 95 6 EMP2 Rey WOES ee terne ped die tie Ute et bene 172 9 5 7 DEI KSyWOIdS edt eR i e tedio date M petes pur 173 95 8 CIS Key WOIGS ied ertt airain E e Aa ia RAE pete ERRAT 179 9 5 9 Geometry Optimization and Transition State Keywords 179 9 5 10 Intrinsic Reaction Coordinate IRC Keywords 185 9 5 11 Solvation Keywords ieies Peor eto terrse stro nE i e 187 9 5 12 Properties Key WOFdS xou entere teen tet tert teretes eR Un 188 9 5 13 Frequency Related Keywords eene 191 9 5 14 Basis Set Keywords el ene tritt iret r re si noii rine seerste 193 9 5 15 Keywords for SCF Methods 2 peret ite setangeaataceas das 193 9 5 16 Initial Guess Key words d e esee qase edie 198 9 5 17 Localization Key WOIGS 1 eiie t de i Pee tape ert meret 200 9 5 18 File Format Conversion Keywords eee 201 975 19 Standard Output Keywords tecti tertie rete 204 Jaguar 5 5 User Manual vii Contents 9 5 20 File Output Keywords 1 2 erret rte a petes 206
53. 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 corre sponding 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 of the second natural orbital in the calculation If a GVB calculation is performed from a Hartree Fock converged wavefunction the program scf runs twice once to obtain the HF converged wavefunction and once to perform the final GVB calculation The SCF output from the first scf 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 6 3 4 GVB RCI For restricted configuration interaction calculations the SCF output is the same as for non RCI GVB calculations but the output from the program rci appears after the SCF output The RCI output first lists information on the total number of orbitals the number of core orbitals for the RCI calculation the numbers of open shell and G
54. 9 The Jaguar Input File The real valued parameters for solvation calculations which are shown in Table 9 22 help describe the solvent and the solute Section 4 5 on page 58 contains more details on these parameters The default values for these parameters correspond to water For solvated geometry optimizations the trust keyword which is described in Section 9 5 9 on page 179 has a default value of 0 1 instead of its usual default of 0 3 Table 9 22 Real valued Solvation Keywords Keyword Default Value Description epsout 80 37 Outer dielectric constant of solvent epsin 1 0 Inner dielectric constant of solvent 138 radprb 1 40 Radius of solvent probe molecule sconv 1 5 x 10 Solvation energy convergence criterion in Hartrees esolv any number Gas phase energy of molecule in Hartrees used in some restart new input files for solvation jobs 9 5 12 Properties Keywords Various keywords are used to request calculation of molecular properties including multi pole moments and charge fitting properties Most of the keywords listed in Table 9 23 correspond to GUI options described in Section 4 6 on page 60 Only the values listed in the table are allowed Table 9 23 Integer valued Keywords for Charge Fitting Multipole Moment and Polarizability amp Hyperpolarizability Calculations Keyword Value Description icfit 0 Do not do electrostatic potential fitting 1 Fit electrostatic potential to atomic centers d
55. 9 10 on page 227 or for input to GAUSSIAN 92 guess cards 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 where the option requested under When was after SCF iterations and the option requested under What was occupied orbitals Only the first two occupied orbitals are shown in each case and not all functions are shown these gaps are indicated by For the How option large elements as f5 2 labels in list 1 Orbital Energy 20 555133 Occupation 1 000000 Symmetry A1 S Oo 0 99 2 Orbital Energy 1 345597 Occupation 1 000000 Symmetry A1 S S Z S Oo 0 21 0 47 0 09 0 42 S H1 0 15 S H2 0 15 3 Orbital Energy 0 713206 Occupation 1 000000 Symmetry B2 Eses For the How option all elements as f10 5 labels in table 1 2 3 eigenvalues 20 55513 1 34560 Fadal 10 S 0 99466 0 21055 20 S 0 02122 0 47102 ae 50 Z 0 00155 0 08586 60 S 0 00430 0 41777 asa 16 H1 S 0 00000 0 14851 eer 21 H2 S 0 00000 0 14851 ese 25 H2 Z 0 00025 0 01342 Jaguar 5 5 User Manual 135 Chapter 6 Output For the How option all elements as f19 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 0038
56. 9 5 21 Output Keywords for Each Iteration sse 207 9 5 22 Orbital Output KeySVOtds eie rrt eie tert reet egeo erp 208 9 5 23 Grid and Dealiasing Function Keywords sess 210 9 5 24 Memory Use ISGyWOEIS iced detnr rire er ee meine thee nre 212 9 5 25 Plotting Keywords eee rre He Ee S Yee R SERE ath ea FT e re kun 214 9 6 The ayp SOCOM aue omini rnt eR FR UR UR re ta ORE US 216 977 Thedmp323 SectioD idet eee re ertet te repetere er errare Fe canes 217 9 8 The atomic Secu Oth ee ese eeu pie ER EHE RE de ede died a olan eee 218 9 8 1 General Format of the atomic Section sees 218 9 8 2 Keywords That Specify Physical Properties eesesss 220 9 8 3 Basis Grid Dealiasing Function and Charge Usage for Individual Atoms 221 9 8 4 Defining Fragments 2 tnnt ete eti i sera rede 225 DOTS NESS Seco crues etre Eee rere e rtr s eerte toe deme rien e exeo ds 226 9 10 The guess Sectores peret ret eto eene dee Se celeres ee etn 227 9 11 The pointely Section cio cscs ects a eee ertet este een Male Sines eee 229 9 12 The efields Section iere perire er dient Usain staves 229 90 15 The ham SecUOfi conet er rete er reete eir retis Eo eee 230 9 14 Th OLDMAN SeCUQD ied re eterne tren eerte De etre ere ape AEA 230 9 T Th eclio Se HOO idet terere tee peores repeat reete pR E ee EE TREE eps 231 9 16 The path Sectio doter reet rere eater e
57. AO space and using the AO space matrix elements to produce the matrix elements in the natural orbital space 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 N 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 integrals A are evaluated in spectral space see Equation 2 The Coulomb matrix elements J s are then evaluated in physical space for all y corre sponding to orbital products of each RCI pair Ypa Whos VpeYpu and V Ypu using the equa tion Jysg Y encisAus 15 ki These matrix elements are transformed into spectral space to form J y where i and j are basis function indices using the pseudospectral method in the usual manner described in Section 8 1 on page 147 Fig Gali ua Rs 16 where Q is the pseudospectral least squares operator and R is the value of the basis func tion j at grid point g A final two index transformation ere 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 iterat
58. Coordinate Calculations Intrinsic Reaction Coordinate IRC calculations can be used to check that the given tran sition state is the expected transition state for the reaction of interest IRC calculations start at a transition 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 orthogonal to the path are optimized The calculations can run in the forward direction toward the products and the backward direction toward the reactants IRC scans have been implemented in Jaguar using the methods described in ref 143 The implementation includes both IRC and minimum energy path MEP calculations The difference between the two is that the reaction coordinate for the IRC path is mass weighted whereas the reaction coordinate for the minimum energy path is not To set up a default IRC or minimum energy path calculation you must first perform a tran sition state calculation and read in the restart file then choose intrinsic reaction coordi nate or minimum energy path from the Optimization task menu of the Geometry Optimization window The calculation also requires a Hessian for the transition state You can either precalculate the Hessian and read it in from the restart file or make the calculation of the Hessian part of the IRC or MEP calculation by including the keyword inhess 4 in the gen section of the input file us
59. Describe the MPICH configuration Table 13 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 specified 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 The secure server can also be launched manually on each machine with the command usr lib mpich bin serv_p4 o p port You can also launch the secure servers within a job by setting the environment variable SCHRODINGER_MPISTART in the shell in which the job is launched in addition to MPI_P4SSPORT and MPI_USEP4SSPORT The value yes requests a single attempt to launch the secure servers An integer value specifies the time limit in seconds for attempts to launch the servers which are made every 10 seconds By default the secure servers are not launched within the job The servers continue to run after the job is finished 294 Jaguar 5 5 User Manual Chapter 13 Parallel Jaguar 13 1 2 4 Selecting Nodes for a Job Job queuing software such as 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 f
60. G6r PO 8r 8V Lv Pd Op QW Sp prL b OW THAN IP JZ Op A 6 IS Bela LE ILOT 60 C COLT SII C OPET c6I C ISET SPLIT LIV T 9c 989p T OSET TIST CLOT Z88 T LE97T OOL T 9061 IM 9tI d St 9S vt SV ECOD Ct D IE UZ OCENO 6C IN 8600 LTA 9c UIN SCHO vC A tC lL TEOS ITED OTA 6l veel ELOT 0061 ELOT LVUC 6vc C OIS I I6FI IV 8I ID LIS 9I d SI IS TI IV el SIN CL EN II Tc9 T 89 T 009 I 009 T 0067I TOT LE T OTTI N OH 6 0 8N LD 9d ed pH ISTI OSTI 9H T H I suouvjnojvo UONDAJOS AOL SJUPWUUSBISSD snippa spoA 42p UDA uo UOYYULLO Ul 240i iof apf DIDP sia 11np op ay pup QQ UO cr uoyoeg aag sdno48 jpuouounf U10149 U1 sui0gD 40f pHs sjsn pp amp jjm42u238 APND DUIS S911011 pjoq U1 UMOYS 240 MO AG sanjva snippa ASOYM SWOID 40f pau81sspa4 AG UVI nppy suoupjnojv uouvajog 40f suo41s8uy ut py SIDA 42p UDA SPS 21qu 223 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File orl LYI 81 OT vel OET LUT OTT 8CI OCT YET PHT 69 1 861 SET Id 8 dd c8 LL IS SH OS8 hV 6L d 8LI LL SO 9L W SLIM PLIL LJH CL I LC ed 9 9D SS Tet cel 9 I OPI IVT prt SPI vel 8c STI Sct LUL OST vel SVT COT I61 OTS 9X PSII ES L cce ds IS US OS UI 6b PO S8t 9V Lb Pd Op UH SPINA Prl
61. Group MOLECULE pKa calc pKa exp Deviation 3 3 dimethylsuccinimide 8 8 9 5 0 7 dimethadione 7 5 6 1 1 4 phthalimide 8 5 9 9 14 succinimide 9 1 9 6 0 5 BARBITURIC ACIDS 5 5 methylphenylbarbituric 7 5 7 4 0 1 1 5 5 trimethylbarbituric 7 8 8 3 0 5 hexobarbital 7 6 8 2 0 6 5 5 dimethylbarbituric 7 6 8 0 0 4 1 5 dimethyl 5 phenylbarbituric 7 8 7 8 0 0 TETRAZOLES 5 cyclopropyltetrazole 5 0 5 4 0 4 5 methyltetrazole 5 0 5 6 0 6 5 hydroxytetrazole 5 1 5 4 0 3 5 phenoxytetrazole 4 7 4 4 0 3 5 phenyltetrazole 4 9 3 5 1 4 tetrazole 4 9 4 9 0 0 PRIMARY AMINES methylamine 10 5 10 2 0 3 ethylamine 10 9 10 6 0 3 propylamine 10 6 10 6 0 0 t butylamine 10 8 10 7 0 1 2 aminoethanol 9 8 9 2 0 6 1 2 ethanediamine 10 1 10 7 0 6 1 3 propanediamine 10 0 10 9 0 9 Jaguar 5 5 User Manual 311 Chapter 14 The pKa Prediction Module Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group MOLECULE pKa calc pKa exp Deviation SECONDARY AMINES dimethylamine 10 9 10 7 0 2 diethylamine 11 0 11 0 0 0 azetidine 11 2 11 3 0 1 pyrrolidine 11 1 11 3 0 2 piperidine 11 0 11 1 0 1 morpholine 9 3 8 5 0 8 2 5 diazahexane 9 3 10 4 1 1 TERTIARY AMINES trimethylamine 10 0 9 8 0 2 triethylamine 10 5 11 0 0 5 tripropylamine 9 3 10 7 1 4 1 methylpiperidine 10 3 10 2 0 1 triallylamine 7 0 8 3 13 1 allylpiperidine 9 8 9 7 0 1 dimethylcyclohexylamine 10 6 10 7 0 1 dimethylbenzylamine 8 9 9 0 0 1 diet
62. Hessian which must either be entered in the hess section or calculated analytically before proceeding with IRC 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 Jaguar 5 5 User Manual 185 Chapter 9 The Jaguar Input File Table 9 20 Keywords for IRC Calculations Keyword Value Description irc 0 Do not do IRC calculation 1 Do IRC calculation with non mass weighted coordinates mini mum energy path scan 2 Do IRC with mass weighted coordinates ircmode 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 direction 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 ircstep 0 1 Step size taken for each IRC point Units are bohr amu or radians amu 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 If a Hessian is entered in the hess section whether directly or from a restar
63. Keyword ip121 2 in gen section of input file 22 Keyword ip122 2 in gen section of input file 23 Keyword ip123 2 in gen section of input file 24 Keyword ip149 2 in gen section of input file 132 Jaguar 5 5 User Manual Chapter 6 Output 6 7 Output Options for Orbitals Orbital information can be printed to the output file as well Several possible choices are available in the Orbitals window whose button is found in the Output section for what when and how orbitals should be printed If you choose to print out orbital information the output from the program pre lists the non default options chosen above the molecular geometry output from the same program and indicates the keywords referred to in foot notes throughout this section When The following When menu options determine the point at which orbitals are printed out after HF initial guess Print orbitals used for the HF initial guess after GVB initial guess Print orbitals used for the GVB initial guess 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 orbitals printed depends on whether five or six d functions are specified for the basis set as described in Section 4 8 on page 70 each iteration in AO space Print orbitals after each SCF iteration in atomic orbital spa
64. 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 is used for the job 5 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 For instance if you want to perform a relaxed scan finding minimum energy geometries while holding a particular coordinate fixed to various values you can set up a geometry optimization input file with a description of the values that coordinate should take Jaguar 5 5 User Manual 93 Chapter 5 Optimizations and Scans If you want to vary a particular coordinate for 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 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 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 of 30 takes 5 steps 0 30 60 90 and 120 To scan over a coordinate set the coordinate with a variab
65. RCI 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 or GVB RCI geometry optimization on a molecule with equal resonating bonds like the carbon bonds in benzene you should force the optimizer to keep their bond distances the same even if the input lists different bond orders for the bonds To impose this restriction use Z matrix form for your geometry input and set all relevant bonds equal to the same variable See Section 3 2 5 on page 29 and Section 3 2 6 on page 31 for more information v no pair sigma v Istpi v lone pair v 2nd pi RCI pair selection User selected OK Cancel Help Figure 4 3 The GVB window 56 Jaguar 5 5 User Manual Chapter 4 Options 4 3 1 GVB or GVB RCI Pair Input In order to describe the placement of GVB pairs for a GVB calculation you need to know the atom numbers for the relevant atoms To display the atom numbers in the Maestro Workspace choose Atom Labels from the Display menu select Atom Number in the Composition tab then click the All button in the Label Atoms group box You can also use the Edit Geometry window and identify the atom number by the order the atoms are listed in the file You can select GVB pairs in any order To specify the first GVB pair leave the Pair slider set at 1 Next specify the desired pair type by clicking in the appropriate box You can choose
66. Table 9 19 All values must be set greater than or equal to 0 Table 9 19 Geometry Convergence Criteria Keywords Keyword Default value Convergence Criterion For gceonvl 4 5 x 10 Maximum element of gradient gconv2 3 0 x 104 rms of gradient elements gconv3 1 0 x 10 Maximum Newton Raphson step not currently used gconv4 1 0 x 107 rms Newton Raphson step not currently used gconv5 1 8 x 10 Maximum element of nuclear displacement gconv6 1 2 x 10 rms of nuclear displacement elements gconv7 5 0 x 10 Difference between final energies from previous and cur rent geometry optimization iterations 184 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 9 5 10 Intrinsic Reaction Coordinate IRC Keywords IRC scans have been implemented in Jaguar using the methods described in ref 143 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 energy surface They are mainly used to check that the given transition state is indeed the expected transition state for the reaction of interest The keywords for IRC and MEP calculations are listed in Table 9 20 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
67. 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 3 4 on page 34 and use it to continue on with the calculation possibly after making some changes to the calcula tion 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 from the Methods window whose button 142 Jaguar 5 5 User Manual Chapter 7 Tips and Suggestions appears in the main window Similarly if you want to perform an additional 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 3 4 on page 34 contains information on reading input files in the GUI See Chapter 9 if you would like more information on input files Note that if you restart a run you may not get exactly the same results as you would if you had s
68. To reset a default radius for hydrogen for instance you could put the following line before any other descriptions of hydrogen atoms 1 1 1 1 1 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 10 3 The description of the atom s bonding type uses the groups listed in the bonding type information described in Section 10 6 1 on page 255 unless it is 1 Any positive integer for bonding type describes the number of bonds the atom has in each of the bonding type groups for its element 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 10 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 that carbon atom had four bonds from carbon s Group 1 bondin
69. User Manual 95 Chapter 5 Optimizations and Scans 96 Jaguar 5 5 User Manual Chapter 6 Output The output from a Jaguar run always includes a Jaguar output file which contains the primary output and a log file which contains a job summary that is updated as the job is being run If you request other output options in the Files window various other files can also be generated as output This chapter begins with a description of the Jaguar output file for a standard Hartree Fock calculation and continues with a discussion of the changes in the output for various other calculation options and the output options that can be set from the Standard Files Per Iter ation and Orbitals windows found in the Output section 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 6 1 Summarizing Jaguar Results You can obtain summaries of Jaguar results in simple table form by using the following command 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 or
70. a sigma bond pi bond second pi bond in a triple bond or lone pair If you select a lone pair it is assigned to a single atom so when you specify the number of the atom for the lone pair using the Atom 1 slider or by clicking in the slider box the same number is displayed for Atom 2 If you select any other kind of pair you must set the atom number for Atom 2 separately The appropriate atom labels for example H2 appear to the right of the Atom 1 and Atom 2 slider boxes Additional GVB pairs can be specified in the same way as the first pair after changing the number shown by the Pair slider A particular atom should have either all or none of its lone pairs specified as GVB lone pairs Also you cannot set GVB lone pairs when you are using a minimal basis set e g STO 3G If you compute solvation energies using GVB or LMP2 as described in Section 4 5 on page 58 we recommend using heteroatom pairs for the GVB calculation for the most effi cient results since solvation energy calculations often use radii optimized for calculations with heteroatom pairs set See Section 10 6 on page 253 for more details Heteroatom pairs are all pairs whose atoms are of different elements except for C H pairs You can select RCI pairs in two ways By default RCI is off for all pairs and the RCI pair selection option menu is set to user selected In this case a pair is included in an RCI calculation only if you select RCI for this pair besid
71. agrees with that described in Chapter 9 Jaguar 5 5 User Manual 269 Chapter 11 Running Jobs Table 11 4 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 username remote jobs Must be used with HOST job submission host WAIT Wait for the Jaguar job to finish before Return to the command prompt returning to the command prompt immediately Replaces w SAVE Save temporary files and temp directory Temporary files are cleaned out of for job at end of job Replaces s temp directory and temporary directory is removed at end of job 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 Replaces n nice 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 t Write time stamps to the log file after Write time stamps to the log file at each executable has run the 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 You can run a single Jag
72. and GVB RCI calculations and calculations of IR intensities or hyperpolarizabilities symmetry is not yet imple mented and is disabled automatically during the job 4 10 Surfaces The Calculate Surfaces window allows you to generate electrostatic potential electron density spin density and orbital data that can be visualized using the surface options in Maestro To generate surface data you must first run a calculation on the molecule of interest and then read in a restart file Once you have read in the restart file the Surfaces button in the Jaguar panel is activated You can generate plot data for the electrostatic potential electron density electron spin density and orbitals in the same run To select multiple orbitals from the list use SHIFT to 88 Keyword locpostv 0 in gen section of input file 89 Keyword locpostv 1 in gen section of input file 90 Keyword locpostv 2 in gen section of input file 91 Keyword isymm 8 in gen section of input file 92 Keyword isymm 0 in gen section of input file Jaguar 5 5 User Manual 79 Chapter 4 Options select a range of items and CTRL to select or deselect a single item without affecting other items The plot data is tabulated on a rectangular grid The box containing the grid encom passes the van der Waals radii of all atoms in the molecule You can adjust the box size within the range 1 to 425 and you can change the density of grid points within the range 1 25
73. and multip keywords in the gen section For more informa tion about the atomic section see Section 9 8 on page 218 After saving the input file with the iguess setting and atomic section you can run it in Jaguar in the usual manner 7 1 2 GVB Calculations GVB Pair Selection 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 9 5 5 on page 170 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 pair 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
74. 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 currently allowed are shown in Table 9 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 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 description or may allow a general string like a file name 162 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 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 optimization tvec Specify reaction coordinate at transition state for IRC calculations gen Sets genera
75. be EE oen 86 5 2 1 Freezing All Bond Lengths Bond Angles or Torsional Angles 86 25 2 2 Freezing Specie CoOTdIBles e de edet ete ee 86 5 2 3 Applying Constraints by Using Variables eee 87 5 2 4 Applying Dynamic Constraints eese enne 88 5 9 Transition State Optmizations cniinne sinirine ee HER erede ere E aS 88 5 3 Transition State Search Method eese teen 89 5 3 2 Specifying Different Structures for the Reaction ss 90 5 3 3 initial WS T CIUe88 e erre rte eom t Heo apte Cet Fore en buen 90 5 3 4 Searching Along a Particular Path or Eigenvector 91 5 3 3 Bigenvector Follow ederet d per Pedes 91 Jaguar 5 5 User Manual v Contents 5 3 6 Refinement ot the Initial Hessian note HR 92 5 3 7 Specifying Coordinates for Hessian Refinement sssss 93 DA Geometry SCANS m abana tenes E a 93 5 5 Intrinsic Reaction Coordinate Calculations eene 95 Chapter 6 OUP e 97 6 1 Summarizing Jaguar Results essent 97 6 1 1 Reporting Final Results From One or More Jobs 100 6 1 2 Reporting Intermediate Results uceiocaee eite 101 6 1 3 Reporting Results for Each Atom eee 102 6 2 Output From a Standard HF Calculation eene 102 6 3 Outp
76. button in the Jaguar panel You can read Jaguar input files or files generated or used by other programs that are recog nized by the file format conversion program Babel 24 Most of these files can be used to provide only geometries Files that can provide other information are explicitly identified in the text below The Read File window contains the usual file browsing tools a Filter text box a Directo ries 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 To select a file type choose from the File Format list The default format is Jaguar input 3 4 1 Reading in Geometries Only You can read a geometry molecular structure from any of the supported file types To read only the geometry and set all calculation settings to their default values choose Geometry new job from the Read as list To read only the geometry and retain the current calculation settings choose Initial geometry from the Read as list When you read in a geometry from a file Jaguar also tries to obtain information on the molecular charge This information is always obtained for Jaguar input files but might not be obtained for other file types For non Jaguar input files check the molecular charge setting in the Molecular State window after reading in the geometry 34 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Filter zone1 juliem jaguart
77. 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 Cundari Stevens ECP basis set 95 named CSDZ has been provided to cover the lanthanides This basis set uses a relativistic effective core potential for the inner core elec trons and treats the outer core and valence electrons with a 4s 4p 2d 2f basis set The ECP basis set developed by Ermler and coworkers 96 101 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 Jaguar 5 5 User Manual 73 Chapter 4 Options been uncontracted Polarization and diffuse functions for the 4p 5p and 6p elements have been added from the relativistic all electron double zeta set of Dyall 103 This addition represents a change from the previous definition of the basis set in which the addition of a or to the basis set name had no effect for the p block elements defined by ECPs Consequently results obtained using the current release with polarization or diffuse func tions on the ERMLER2 basis sets may differ from results obtained with previous releases Table 4 4 describes the ECP basis sets The atoms described by the effective core potentia
78. 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 10 5 on page 252 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 9 5 23 on page 210 and Section 10 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 matrix 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 DIIS error vector For HF calculations 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 If you are not running a default single point Hartree Fock calculation the log file g
79. calculated analytically 1 Atomic analytic corrections of the form lt aalaa gt calculated for K 2 Diatomic analytic corrections of the form lt aalaa gt lt aalab gt lt aalbb gt and lt ablab gt calculated for K a a b andc refer to distinct 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 the Lewis file are described in Section 4 5 on page 58 and Section 9 8 on page 218 and are listed in Table 9 43 on page 223 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 1lewis file from the data directory unless you specify your own lewis file in a LEWISFILE line in the input file as described in Section 9 1 on page 161 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 hybridization 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 de
80. 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 the jaguar command is jaguar command options where command is any of the commands listed in Table 11 1 The options may be given in any order and may precede any options specific to the command 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 h2o jaguar run h2o in both run a Jaguar job with the job name h2o and the input file h2o0 in 266 Jaguar 5 5 User Manual Chapter 11 Running Jobs Table 11 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 Start the Jaguar
81. 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 57 van der Waals radii for hydrogen and for carbon through argon and universal force field 54 van der Waals radii for all other elements These radii are listed in Table 9 42 and can be changed using the vdw keyword The van der Waals radii for solvation calculations are listed in Table 9 43 and can be changed using the vdw2 keyword The radii for the elements H C N O F P Cl Br and I can be adjusted by Jaguar in some functional groups See Section 10 6 on page 253 for more information on how Jaguar uses these radii in solvation calculations The covalent radii used to determine which atoms are bonded are given in Table 9 44 Two atoms are considered to be bonded if the distance between them is less than covfac times the sum of their covalent radii where covfac is a keyword with a default value of 1 2 These radii can be changed using the cov keyword See page 125 and Section 9 5 1 on page 168 for more information on how Jaguar uses and presents covalent radii and bonding information 9 8 3 Basis Grid Dealiasing Function and Charge Usage for Individual Atoms The basis keyword allows you to specify the basis sets used to treat particular atoms The string provided to describe the basis set should be chosen from the first column of the tables in Sectio
82. criterion DIIS is started when the largest value of the DIIS error vector is less than the value of stdiis whose units are hartrees For standard Hartree Fock DFT LMP2 or GVB LMP2 calcula tions stdiis is 2 0 by default for GVB calculations when iconv listed in Table 9 27 is 3 or 4 stdiis is 1 0 by default and for cases involving transition metals or open shell calcu lations or when the initial guess is obtained from the one electron Hamiltonian iguess 0 see Section 9 5 16 on page 198 its default value is 0 1 In general after GVB DIIS starts any density matrix averaging requested by the keywords iteravg and istavg explained in Table 9 27 is turned off The last real valued methods keyword vshift describes the amount the virtual orbitals energies are increased before diagonalization 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 calculations 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 other integer SCF keywords are described in Table 9 27 Note however that the keyword settings for convergence are somewhat complicated and the defaults vary some what depending upon the settings of other keywords Table 9 27 Integer Keywords for Methods Used in the SCF Convergence Procedures Keyword
83. 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 Lead zeros 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 accu racy to be used for the calculation The first line provides the information necessary to run a calculation with all ultrafine pseudospectral grids and with tight cutoffs and corre sponds to an accuracy level setting of ultrafine from the GUI as described in Section 4 9 5 on page 78 or to the keyword setting iacc 1 in the gen section of the input file as described in Section 9 5 15 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 iterations The cutoff sets themselves are provided later in the file and dictate the level of analytic corrections the grid and the non default values of the gen section cutoff keywords cutl 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 iterati
84. default The fit can be constrained to reproduce exactly the dipole moment and other higher moments if specified by choosing charge dipole moment or the appropriate higher moment choice from the ESP constraints option menu For LMP2 wavefunctions only dipole moments are available Keep in mind that the more constraints you apply to elec trostatic potential fitting the less accurately the charge fitting will describe the Coulomb field around the molecule The dipole moment is generally very close to the quantum mechanical dipole moment as calculated from the wave function and constraining the charge fitting to reproduce it 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 36 Keyword incdip 1 in gen section of input file 37 Keyword incdip 2 or 3 in gen section of input file Jaguar 5 5 User Manual 61 Chapter 4 Options 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 An alternative is to use
85. energy evaluation you should not perform a geometry optimization or calculate the solvation energy polariz ability or any other properties 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 4 1 on page 49 Table 9 15 Functional Coefficient Keywords Keyword Corresponding Functional or Exact Exchange xhf exact exchange Hartree Fock xexl1 Slater local exchange functional xexl9 Xo 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 1 local and nonlocal exchange functional xexnl9 PBE local and nonlocal 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 correlation functional xcornl1 Perdew 1986 non local gradient correction xcornl2 Lee Yang Parr local and nonlocal correlation functional xcornl3 HCTH407 local and nonlocal correlation functional xcornl4 Perdew Wang G
86. fempdir processors number of processors schrodinger installation path The settings are described in the following sections A full list of settings including settings for batch queue configuration is given in the Schr dinger Product Installation Guide A setting in the schrodinger hosts file can be formatted with any combination of spaces and tabs but the entire setting must be on one line Comments may be included in the schrodinger hosts file and should start with a hash sign 264 Jaguar 5 5 User Manual Chapter 11 Running Jobs If you have installed Jaguar on multiple machines you might need to edit the schrodinger hosts file on each machine to add entries for the other machines 11 1 1 The name and host Settings The name setting must be the first line for each machine This is the name that is displayed in the list of known hosts in the Job Host menu of the Jaguar Run window Usually entry label is the name of a machine a host that can be used to run a Jaguar calculation but if it is not you must include a host setting that supplies the machine name The host setting is only needed if the name line does not give the machine address You might for example want to provide an alias in the name setting and define the host name in a host setting if the host name is long Another possible use of multiple entries for a single machine is to specify different settings on a machine such as different scratch directories or di
87. 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 in van der Waals contact Other wise small changes in a torsional coordinate far away from these atoms can then lead to steep changes in the energy Adding explicit coordinates for these non bonded contacts makes it possible for the optimization algorithm to control their approach more effectively 166 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 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 9 5 9 on page 179 for more details To specify that particular bonds or angles should be included in the internal coordinates generated 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 coor dinate to be included among the internal coordinates generated by Jaguar If you want to hold the coordinate fixed at its initial value throughout the job add the entry to the end of the line after one or more spacing characters As an example the coord sectio
88. functions 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 instance 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 function a p type function resulting from the deriv ative 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 func tions 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 th
89. given in the guess section is for the this basis set Otherwise a poor or meaningless guess is obtained 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 coefficients in the guess section This next line of the section should begin with a set of coefficients describing the contribu tion 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 unimpor tant 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 6 7 on page 133 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 section of the input file for the first run as describ
90. how to specify bond length or angle constraints on the Z matrix coordinates for geometry optimizations 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 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 Z matrix format geometries Finally if you are optimizing a molecular structure to obtain a minimum energy structure or a transition state you might want to refine the Hessian used for the job See Section 5 3 on page 88 for information on the methods used for transition state optimizations including Hessian refinement If you put 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 slightly and will use the results to refine the initial Hessian to be used for the optimization To request refinement of a coor dinate 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 run with this zmat section amp zmat O1 H2 O1 1 419 H3 O1 T4 H2 108 0 amp that included Hessian ref
91. i ese ede es 231 9 17 The plot Section o roe ether tpe E eee E Rede oE i erano 234 9 18 INBOESGGUOS re n lestie cesses ERAI Ro UR URP A RH E seen ade 236 Chapter 10 Other Jaguar Files e eeeeee eere eese e eee nennen sten tna enun 237 10 T Whe Basis Set FIG ue terrre Er Ene Ree RE ree ER RR ERR EEEE Derek ih 237 10 1 1 Format of the Basis Set Pile oie ettet 237 10 1 2 Customizing Basis Sets eene eret etr ennt tna niite 241 10 2 The Initial Guess Data File iei reet iet tein 242 10 3 The Dealiasine Function File e rere e tere erect 243 10 3 1 File Format and Description eere treten eire 244 10 3 2 Sample FS s s seeria E Aa ES E EAE bearers leds 247 104 The Grid File sissien eter etuer eerte eon eie Fist Ei ans sS e tee E s 248 10 4 1 File Format and Description eeeeseeeeeeeeneeeeeenneennen 249 10 5 The C utot File ossia er ne nt ere E E echa 252 10 6 The Wie wig File serien eere E A 253 10 6 1 Describing Bonding Types in the Lewis File sss 255 viii Jaguar 5 5 User Manual Contents 10 6 2 Describing Hybridization Types in the Lewis File 256 10 6 3 Setting van der Waals Radii From Lewis File Data 258 10 6 4 Default Behavior for Setting Radii eee 262 Chapter 11 Running Jobs 4 eee eese eere rete eene tnnt ntn sator tn enata tnann 263 11 1 C
92. in ZAM ALEK inet teh sareevetecs 29 output keyword esse 205 bonding types describing in lewis files 255 Boys localization see 79 input keywords for 173 200 orbital printing 123 133 200 209 Output from decis eiecit 123 Build panel etes 9 330 C calculation host 269 285 286 definition dede eer ebrei 265 entries in schrodinger hosts 265 Sel Cltig een nein 39 270 canonical orbital space output in eee eects 132 135 208 209 Cartesian coordinates format for geometry 27 28 29 164 freezing for geometry optimization 29 86 87 CN progran essesi nanii 232 output from 112 113 116 121 charge fitting see ESP fitting Mulliken population analysis charge atomic from ESP fit inocentes keyword for formal charge molecular Key WOIS iacebat eatenus 169 setting in Maestro sese 33 charges atomic Mulliken iecit 64 chdens electron density output file eiie 63 119 120 189 CIS calculations essese 75 179 CU S progra Adan Ie n o er en 232 Cleanup button eere 36 Command Input Area sees 6 command options jaguar run 270 comment line batch script ees 276 input file cunnis 40 45 162 configuration interaction CI CI singles calculations 75 179 energy lowerin
93. integer indicating the number of orbitals in that shell 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 Jis not a core orbital 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 9 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 i j k 1 p end amp where i j k and are integers indicating the ith jth kth and th orbitals before mixing i e Xi Xj Xi and Xj and ot and D are angles in degrees indicating the degree of mixing The command hfiglcmo mixes the orbitals to form orbitals x7 q Xg and Xi according to the following equations new i X Cosa X sino new j XjC0s0 X sinat 230 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File new Xe X cosB x sinp new x cosB x sinp T 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 orb
94. internal coordinates for the optimization Conse quently 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 9 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 4 and Chapter 6 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 solution calculation of various molecular properties basis sets SCF methods and output These subsections correspond to the order of information in Chapter 4 and Chapter 6 Finally keywords relating to grids and dealiasing functions cutoff parameters and memory usage are described 9 5 1 Geometry Input Keywords The keywords iunit and covfac help determine how the geometry input from the zmat section will be interpreted The iunit keyword whose default value is 1 describes what units the geo
95. is described in Section 9 5 16 on page 198 GVB pairs are set in the gvb section where pairs to be used in an RCI restricted configu ration 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 You can find Lewis dot structures by setting the appropriate keywords and you can also use one of these structures to set GVB pairs automatically The appropriate keywords are listed in Table 9 6 The Lewis dot structure code finds several alternative Lewis dot structures for resonant molecules 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 simply set igvball and igvbsel At that point lewdot and lewstr will be set to 1 by default 170 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 6 Keywords for Evaluation of Lewis Dot Structures and Application of That Informa tion to GVB Pair Settings Keyword Value Description lewdot 0
96. is described in Section 8 5 on page 159 This section describes how to set up a DFT calculation in Jaguar You can perform DFT geometry optimizations solvation calcula tions charge fitting and all other calculations and properties available for Hartree Fock wave functions You can also specify functionals to use for a non self consistent DFT eval uation of the energy of an HF or GVB wavefunction Jaguar 5 5 User Manual 49 Chapter 4 Options Grid density medium DFT Model Hybridization Exchange Slater Becke 88 Local Correlation Nonlocal Corr LYP L NL OK Cancel Help Figure 4 1 The DFT window 4 1 1 Stage and Grid Density By default the Stage setting is SCF meaning that Jaguar performs an SCF calculation of the Kohn Sham orbitals and DFT energy If you set Stage to Post SCF Jaguar evaluates the DFT energy of the final wave function using the functionals you have specified You may also choose one set of functionals for the SCF stage and another set for a post SCF DFT energy evaluation by making functional settings for each Stage choice in turn If you do a post SCF DFT energy evaluation on any wavefunction you cannot perform a geom etry optimization or calculate the solvation energy polarizability or any other non default properties The Grid density menu determines the grid for DFT calculations By default DFT calcula tions use grids with a medium point density but finer densi
97. is to include a plot section in the input file See Section 9 17 on page 234 for information on the plot section and its keywords See Section 4 10 on page 79 for information on setting up plot data using the GUI The generation of plot data is incompatible with NBO calculations You must run NBO calculations in a separate job 214 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 40 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 gt 0 Index of first alpha orbital for which to generate data iorb2a gt 0 Index of last alpha orbital for which to generate data Ignored unless iorb1a is positive iorblb 1 Generate data for all beta orbitals 0 Do not generate any beta orbital data gt 0 Index of first beta orbital for which to generate data Ignored for restricted wave functions iorb2b gt 0 Index of last beta orbital for which to generate data Ignored unless iorb1b is positive plotres 2 5 Number of points per unit length The length units are defined by the iunit keyword The defaul
98. iteration The meanings of their possible values are shown in Table 10 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 10 6 The Lewis File The Lewis file determines how van der Waals radii for calculations using the Jaguar solva tion module are set according to chemical functional groups By default for neutral mole cules 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 Jaguar 5 5 User Manual 253 Chapter 10 Other Jaguar Files Table 10 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
99. jobs whose job names are listed using the specified 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 11 3 on page 275 for more information on this com mand Start a Jaguar pKa 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 specified See Section 6 1 on page 97 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 al 1 option shows the status of all jobs including completed jobs The output lists the job ID the job name the status Kill the specified Jaguar jobs or all jobs that have the speci fied status This command is processed immediately Remove records for the specified jobs from the job data base If no jobname is given all completed jobs are purged Stop the specified Jaguar jobs or all jobs that have the spec ified status when the currently running executable has fin ished Report the hardware and software configuration This com mand gives the same output as the SSCHRODINGER machid command Report information on the hardware platform This com mand gives the same output as the SSCHRODINGER platform command List the available batch scripts Report any system requirem
100. kind of initial Hessian Jaguar should generate You can select from among several internal guesses the Fischer Alml f Hessian 50 the Schlegel Hessian 51 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 can be 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 5 1 4 Trust Radius In order to avoid changing the geometry too much because of an unusually shaped poten tial 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 bohr and or radians The trust radius can vary from one iteration to another If the trust radius is marked Fixed the trust radius remains the same throughout the opti mization 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 struc tures If the trust radius is not fixed the default for transition state optimizations Jaguar keeps geometry changes within the region th
101. module is to calculate parts A B and C of the above cycle where upon the actual pK which is related to D by 1 PK 23327 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 BH 5Bg H o The gas phase free energy difference between the protonated and deprotonated states can be computed via the usual relations A AH TAS Eg Esm 5 2RT TAS Evaluation of this expression requires the following quantum chemical calculations 1 Geometry optimization of the protonated and deprotonated species Note that quan tum chemical methods generally carry out a conjugate gradient optimization and hence cannot search for multiple minima We shall assume in this discussion that there is only a single well defined conformational minimum and that a good initial guess obtained for example from molecular mechanics or semiempirical quantum chemistry is available Density functional theory particularly those variants employ ing an admixture of Hartree Fock exchange have been shown to provide good qual ity geometries we utilize B3LYP 6 31G geometry optimization 300 Jaguar 5 5 User Manual Chapter 14 The pKa Prediction Module 2 Accurate single point energies at each optimized geometry must be evaluated These single point calculations are carried out at a sign
102. 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 Z matrix style zmat section should begin with the amp zmat or zmat label and end with a amp or character should not include a line defining any variables which are set in the zvar section described in Section 9 3 on page 166 and should not contain any comment lines but otherwise should have the same format as described in Section 3 2 5 Section 3 2 6 and Section 3 2 7 One additional optional feature is also available from the input file you can orient the molecule or system according to a label on the same line as the amp 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 then assumes the first atom in the Z matrix is at the origin the second is along the a axis in the negative direction for a and the third atom is in the ab plane in the quadrant determined by the positive or negative signs of a and b 164 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Z matrix input is interpreted in the units specified by iunit Section 3 2 on page 26 also includes a description of
103. number of orbitals total 25 number of core orbitals 5 number of open shell orbs 0 number of occupied orbitals 5 number of virtual orbitals 20 number of hamiltonians 1 Jaguar 5 5 User Manual 103 Chapter 6 Output number of shells we s 1 SCF type HF To sx do SA i t pi O LE RMS maximum em di 11 energy density DIIS r t gS t d total energy change change error etot 1 N N 5 M 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 etot 3 Y Y 76 UM 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 5b YY 65M 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 Energy sf se sce er Rh nn 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 A1 1 80256 A2 1 82999 A1 end of program scf The output from the program scf begins with a list of information de
104. optimization and then evaluate the energy of the new structure using LMP2 or DFT techniques To use jaguar batch you need a batch input file whose name should end in bat and at least one template Jaguar input file The batch input file tells jaguar batch how to modify the 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 func tion 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 Jaguar 5 5 User Manual 275 Chapter 11 Running Jobs 11 3 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 11 6 The directives apply to
105. other possible GVB lone pairs on that atom 7 1 3 Geometry Optimization 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 you could start by performing a Hartree Fock geometry optimiza tion then restart the calculation using the HF results in an LMP2 geometry optimization See Section 7 2 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 Jaguar 5 5 User Manual 141 Chapter 7 Tips and Suggestions iterations allowed as set in the Optimization window If it did not reach convergence you can restart the run as described in Section 7 2 7 1 4 Electrostatic Potential Charge Fitting It is probably best not to constrain electrostatic potential charge fitting to reproduce multi pole moments higher than the dipole moment because the errors in fitting the Coulomb field outside the molecule are likely to be high Fitting to the dipole moment is usually safe in fact even without this constraint the dipol
106. other data such as molecular geometries produced by modeling packages Try the sample calculation in Section 3 1 to get some experience running Jaguar and to make sure your system is set up properly If you have problems starting or using the GUI or performing the calculation you may be able to solve them using the troubleshooting suggestions in Chapter 12 If any problems persist contact your system manager or Schr dinger The rest of this chapter describes the basics of using the GUI including entering a geom etry and submitting a job The footnotes describe 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 later 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 using the Edit Job window 3 1 Sample Calculation This section provides instructions on running a sample calculation on the water molecule The sample calculation works only if Jaguar has been correctly installed If the calculation does not work try the suggestions in Chapter 12 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 wri
107. 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 110 Jaguar 5 5 User Manual Chapter 6 Output 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 geometry optimization step from the original geometry and the optimization continues until convergence For transition state optimizations the output for iterations that follow any Hessian refine ment 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 outpu
108. over the processors Each processor runs only one job at a time If there are more jobs than proces sors the remaining jobs will wait until a processor is available If you run multiple Jaguar jobs on a single processor the jobs run sequentially the next job in the script is not started until the current job has finished 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 pKa jobs which can be run on two processors because they consist of two independent jobs You cannot run MPI parallel jobs as batch jobs In addition to choosing a host you can also choose a scratch directory if there is more than one defined for the host in the schrodinger hosts file and you can choose the job directory When you are ready click RUN to launch the batch job When you click RUN the Monitor panel opens This panel 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 automat ically updated as the Jaguar jobs run You can close the Monitor panel by clicking the Hide button If you want to reopen it later choose Monitor from the Applications menu in the Maestro main window 3 7 Saving Input Files You can use the Save window to store a Jaguar input file or to save a geometry in an appropriate format for another program You can later read Jag
109. 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 10 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 321 Table 10 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 294 129 2 8 3 Un 3 2 Stroud p 294 129 3 12 3 U3 3 1 McLaren p 296 129 4 14 5 Un 5 2 Albrecht amp Collatz p 294 129 5 18 5 Un 5 1 Albrecht amp Collatz p 294 129 250 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files Table 10 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 L
110. 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 distri bution of the radial shells The keywords and their settings have the form ndfgrdX1 nr ndfgrdX2 na idferdX pqq amp amp 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 10 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 139 the default for medium fine and gradient grids 2 Becke s Gauss Chebyshev distribution 140 3 described in ref 141 and 4 the Mura Knowles distribution 142 210 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File the default for the 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
111. satisfied with the selection click OK to apply the operation you have chosen with the selection you have made The operation is described in a bar at the top of the Atom Selection dialog box ASD Some operations such as Delete take effect immedi ately Others merely define a set of atoms to be used in a subsequent task such as selecting atoms for creation of a surface While the Atom Selection dialog box is open you cannot perform other actions with the exception of interacting with the structures displayed in the Workspace such as rotation translation and picking 2 6 Toolbar Controls The toolbar contains buttons for performing common tasks There are several kinds of buttons on the toolbar Some buttons perform simple tasks like Fit to Screen or Clear Workspace Other buttons open panels such as the Import panel Buttons that have a small Jaguar 5 5 User Manual 11 Chapter 2 The Maestro Graphical User Interface triangle in the lower right corner have menus that you can open by holding down the left mouse button Some of the toolbar buttons retain the last menu choice and you only need to click them to use that choice Some buttons have different actions depending on whether you click them or double click them You can show or hide the toolbar using the collapse button at the top or from the Display menu and you can hide it or move it to the right or left of the workspace by right clicking in the toolbar and selecting the appr
112. scaling Frequency scaling IR Intensities Thermochemistry Pressure atm Start Temp Temp Increment Number of steps Output units Figure 4 6 The Frequencies window 4 7 4 Frequencies To calculate vibrational frequencies select on compute Hessian in the Frequencies window Vibrational frequency calculations are available for HE GVB LMP2 and DFT wavefunctions in gas phase or in solution but are not available for GVB RCI or GVB LMP calculations 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 4 8 on page 70 for more information on basis sets Otherwise Jaguar uses energies obtained at perturbed geometries to calculate the numerical derivatives of the analytically computed forces Generally 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 geometry optimization for instance then use the new input restart file generated during the job as input for an analytic frequency job See Section 7 2 on page 142 for information on generating restart files and restarting jobs If you want
113. section of input file 21 Keyword iqst 1 in gen section of input file Jaguar 5 5 User Manual 89 Chapter 5 Optimizations and Scans 5 3 2 Specifying Different Structures for the Reaction As mentioned above for a QST guided search you must enter either two geometries corresponding to the reactant and the product or three geometries corresponding to the transition state guess the reactant and the product In either case for best results the reac tant 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 If you are entering three geometries the transition state guess is the main geometry used so the reactant and product geometries are labeled Geometry 2 and Geometry 3 If you enter two geometries the first geometry is the main geometry used and the second is considered to be Geometry 2 The main geometry for the job is the one used to determine constraints and coordinates Constraints in Geometry 2 or Geometry 3 are ignored and the atoms in these geometries must be listed in the same order in which they appear in the main geometry To enter these geometries you can build them in the Maestro Workspace read them or create them in the Edit Geometr
114. sections they are assumed to be the geometries for the reactant in zmat2 and product in zmat3 The forward direction is defined as moving from reactant to product 2 If a vector is entered in the tvec section a new section it defines the forward direc tion An example of such a vector is as follows amp tvec C2 H3 0 5 Ol C2 H3 1 0 amp This definition produces a composite coordinate that is the sum of 0 5 times the bond stretch between atoms C2 and H3 and 1 0 times the angle bend involving atoms O1 C2 H3 The forward direction is the direction that makes this coordinate larger 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 ordinal numbers for the atoms can be used in specifying atoms Coordinate coefficients specified by including an asterisk followed by a value after the last atom are optional The default coefficient value is 1 0 3 The Hessian eigenvector for the imaginary frequency mode with the most negative eigenvalue of the Hessian is used to define the forward direction The phase of the eigenvector is chosen so that the largest coefficient is positive IRC calculations can be done in either Cartesian coordinates specified with intopt 0 in the gen section or redundant internal coordinates intopt 1 which is the default IRC in anything but the downhill mode requires a
115. sgi com products evaluation 2 If necessary install Array Services You can check to see if Array Services are present with the command showprods grep arraysvcs If you have Array Services 3 2 Patch 3532 is required You can check if Patch 3532 is already installed with the command showprods grep 3532 If it is not you can get it from http support sgi com surfzone patches Array Services allows your SGI to run MPI applications like parallel Jaguar Start the array services daemon with the following command etc init d array start 290 Jaguar 5 5 User Manual Chapter 13 Parallel Jaguar The arrayd daemon can be configured to start automatically at system startup with the command chkconfig array on Finally note that a CERT advisory http www cert org advisories CA 99 09 arrayd html has been posted about the default Array Services installation on IRIX versions 6 2 6 5 4 A simple fix is available at ftp patches sgi com support free security advisories 19990701 01 P 13 1 2 LINUX Installation For Linux parallel Jaguar requires the MPICH package Jaguar is now supported under Red Hat Linux 7 3 which is based on a Linux 2 4 kernel Earlier versions might run but are not supported If Jaguar is to run in parallel on a multiprocessor machine the kernel must be compiled for SMP symmetric multiprocessing 13 1 2 1 Installing MPICH We recommend building MPICH from the source code The latest s
116. simply end because it reached the maximum number of SCF iterations a number set in the Methods window 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 Try setting iacscf to 1 2 3 or 4 see Table 9 27 on page 194 for descriptions of each number s function You might need to increase the setting of maxit to 100 or more when using iacscf values of 1 2 or 4 Select GVB DIIS from the Convergence scheme option menu in the Methods win dow Generally DIIS is the better choice but the GVB DIIS convergence scheme sometimes leads to convergence when DIIS does not Set the SCF level shift in the Methods window to 0 5 or 1 0 The higher the setting the more the virtual orbitals energies are increased before diagonalization and the more the mixing of the real and virtual orbitals is reduced High SCF level shifts can slow convergence 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 Jaguar 5 5 User Manual 139 Chapter 7 Tips and Suggestions Change the Accuracy level setting in the Methods window to ultrafine This setting causes the job to use denser pseudospectral grids and tighter cutoffs
117. specified by the FLAGS directive Temporary files generated during the job are written to the subdirectory new name in the scratch directory and output files are written to the current working directory The template job name can either be the stem of an existing input file or the string SJOB If the string SJOB is used the batch script is run multiple times substituting for SJOB the job names that are provided as arguments to the jaguar batch command For example for the job specification h2o h2o0_dft dftname b3lyp the file h20 in is read the keyword setting df tname b31yp is added to the gen section of 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 jobnamel jobname2 jobname3 Jaguar 5 5 User Manual 277 Chapter 11 Running Jobs 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 unl
118. tab you can change the bond orders retype atoms invert structures around chiral centers and make adjustments on individual atoms In the Properties tab you can set properties such as charges partial charges and names of structural units 2 5 Atom Selection Maestro has a powerful set of tools for selecting atoms in a structure that takes advantage of chemical information about the structure These tools are embedded in each panel in which you might need to select atoms to apply some operation Once you have decided which operations to apply you can select or pick the atoms to which you want to apply the chosen operation using the tools provided If you want to select all atoms in a molecule a chain a residue or an entry you can choose a pick state using the Pick list Once you have chosen the pick state you can click on an atom in the Workspace and all the atoms that belong to the same structural unit as defined by the pick state are selected For example if you choose Residue and click on any atom in a glycine residue all the atoms in that glycine residue are selected To select individual atoms choose Atoms from the Pick list The Pick list varies from panel to panel because not all pick states are appropriate for a given operation For example some panels have only Atoms and Bonds in the Pick list If you want to make atom selections based on more complex criteria such as selecting all the carbon atoms in a protein backbon
119. the Opti mization window while both windows are open because the Optimization settings could conflict with your hand assigned constraints 3 2 8 Counterpoise Calculations To perform counterpoise calculations you can use a Cartesian or Z matrix geometry that includes counterpoise atoms which have the usual basis functions for that element but include no nuclei or electrons These calculations can be useful for obtaining an estimate of basis set superposition error BSSE For LMP2 calculations see Section 4 2 on page 54 the LMP2 correction is already designed to avoid basis set superposition error so we advise computing only the Hartree Fock counterpoise correction term To specify a counterpoise atom place an sign after the atom s label For example to place sodium basis functions at the Cartesian coordinates 0 0 0 0 1 0 you could include the following line in an input file Nai 0 0 0 0 1 0 3 2 9 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 5 3 on page 88 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 32 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro or not you refine particular coordinates you can speci
120. the corresponding output is not generated 9 5 20 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 in is created in the temp directory 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 other wise jobname 02 in or jobname 03 in and so on To turn off ip151 you must set it to 0 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 9 32 Many of these options can be turned on from the GUI as described in Section 6 5 on page 129 Additional settings are available for ip160 and
121. the direc tory from which you started the GUI The output file ends with the extension out For instance if you entered the job name h2o the output file would be h20 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 Jaguar 5 5 User Manual 25 Chapter 3 Running Jaguar From Maestro 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 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 the GUI If you were unable to run the sample calculation see the trouble shooting suggestions in Chapter 12 If you want to experiment with the sample calculation use the buttons in the bottom section of the Jaguar panel to open other windows the DFT window for example which you can use to set up a calculation These possible selections are described in Chapter 4 If you don t change any settings in these window
122. 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 11 2 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 11 4 and described below The first three options are common to all Schr dinger programs You can also use the version options listed in Table 11 3 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 3 7 on page 44 for more information If you create or edit an input file using a text editor make sure its format
123. 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 informa tion 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 0 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 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 10 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
124. the window If you select Close and there are unsaved changes you are asked if you want to save them The Revert option lets you return to the original geometry if any in the window when you opened it and Cancel closes the window without retaining any changes made since you last saved a geometry The options in the Structure menu and the Use initial geometry Z matrix option in the Z matrix menu are useful for certain types of transition state optimization jobs but not for other Jaguar jobs These options are described in Section 5 3 on page 88 Edit Geometry EMEN nx File Edit Z matrx Structure 2583000000000 0 0932250000000 0541250000000 2583000000000 1 0256750000000 0541250000000 0 0703000000000 0 4662250000000 9482750000000 0 6675430000000 0 5833490000000 0868020000000 0 6676620000000 1 7022450000000 0869280000000 1 6998300000000 0 2103040000000 8696320000000 0 3393910000000 0 2103040000000 0893380000000 z variables amp zmat and amp zvar sections are combined Figure 3 2 The Edit Geometry window Jaguar 5 5 User Manual 27 Chapter 3 Running Jaguar From Maestro If you edit a geometry and do not save it and you try to run a job by clicking RUN in the Run window or save an input file by clicking OK in the Save window a warning is posted If you ignore the warning and proceed the last geometry saved will be used instead of the edited version 3 2 2 Cartesian Format for Geometry Inpu
125. these references are available from Schr dinger upon request The other list ings in this section are referenced throughout this manual 1 10 11 12 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 Consistent Field Calculations on Polyatomic Molecules J Phys Chem 1988 92 3091 Ringnalda M N Won Y Friesner R A Pseudospectral Hartree Fock calcula tions 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 Application 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
126. 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 h20 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 jJobname 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 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 g92 in a Jaguar input file called h20 in the resulting job would create a Gaussian input file called h20 gzmat g92 You can also convert file formats from the command line using the jaguar babel and jagconvert utilities See Section 11 2 5 on page 272 for information on these utilities 9 5 19 Standard Output Keywords The keywords listed in Table 9 31 are the standard print options They are all set to 1 by default and the result is that none of the information that th
127. this case you should inspect the symmetrized coor dinates in the Edit Geometry window to insure that symmetrizing had the desired effect and did not discard any important information about the molecular geometry When you symmetrize the molecule the comment for the job which is described in Section 3 6 and which appears in the input and output files for the job includes the note Geometry symmetrized to point group followed by the point group name 3 6 Running Jobs You can submit a job either from the GUI or from the command line You might need to submit jobs from the command line if for any reason you cannot display the GUI on your monitor or terminal Information on submitting jobs from the command line with the jaguar run command can be found in Section 11 2 on page 266 This section describes the submission of jobs from the GUI 3 6 1 Starting Individual Jobs Once you have read in a geometry you can submit a Jaguar job by clicking Run in the Jobs section of the Jaguar panel and entering the appropriate information Before you open the Run window close any other open windows to save settings you might have changed The information you enter in the Run window mainly tells Jaguar how and where to launch a job The choices available in the Run window option depend on the schrodinger hosts configuration file See Section 11 1 on page 263 for more infor mation on this file If you do not change the entries in the Run window the
128. to 51 Keyword ifreq 1 in gen section of input file Jaguar 5 5 User Manual 65 Chapter 4 Options calculate frequencies numerically instead make the keyword setting nmder 2 in the gen section of the input file as described in Section 9 5 on page 168 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 choose use available Hessian from the Vibrational Frequencies option menu If you choose to generate a Molden input file after a frequency calculation the normal modes are written to the Molden file enabling you to visualize the frequencies with this program See Section 6 5 on page 129 or Section 9 5 20 on page 206 for more information on writing a Molden input file 4 7 2 Atomic Masses For frequency calculations by default the atomic mass used for each element is that of its most abundant isotope 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 4 7 3 Scaling of Frequencies Because the errors in quantum mechanical calculations of frequencies are often fairly predictable it is sometimes desirable to scale frequencies by one or more factors Scaling methods can also improve calculations of thermochemical properties which use the scaled frequencies In Jagu
129. torsional angles relative to three colinear or nearly colinear angles In such a case you should use dummy atoms to define the torsional angle see Section 3 2 6 on page 31 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 0O4 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 N1 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 30 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro r5 X r24 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 instead of second bond angles if you want to perform a constrained geometry optimization however since Jaguar cannot interpret any
130. twice that of a gas phase calculation Solvation energies can be computed for cases using HF DFT GVB or LMP2 wavefunc tions For GVB or local LMP2 solvation energy calculations we recommend using heteroatom pairs for the most efficient results particularly since solvation energy calcula tions often use radii optimized for calculations with heteroatom pairs set See Section 10 6 on page 253 for more details See Section 4 2 on page 54 and Section 4 3 on page 56 for information on setting LMP2 or GVB pairs 4 5 1 Solvent Parameters Solvent parameters are set in the Solvation window which is opened by clicking the Solva tion button in the Jaguar panel If the solvent you want to use for your solvation energy calculation is listed in the set of choices available under the Solvent option menu you can make the appropriate choice and Jaguar performs a solvation calculation setting the appropriate dielectric constant and probe radius The dielectric constant 52 and probe radius 53 values set by Jaguar for various solvents are shown in Table 4 1 To use a solvent that is not on the list define it by choosing other from the Solvent option menu and changing the entries for Dielectric constant Solvent molecular weight and Solvent density The latter two values are used to calculate the probe radius in angstroms whose value is shown in the same window see reference 53 30 Keyword epsout in gen section of input file 31 Keywo
131. two electron terms the electronic energy and the total energy The orbital energies for the occupied orbitals are also provided for each iteration The Coulomb and exchange contributions to the total two electron energy are printed as well if the J and K matrices are kept separate for the calculation as for GVB calculations and when the Core J and K option in the Methods window is turned on In addition for most calculations involving open shells or higher level methods the individual contribu tions from each Hamiltonian are printed for the Coulomb and exchange terms If the calculation involves solvation the nuclear electronic and kinetic terms making up the one electron terms are also listed as well as the term V T where V is the potential energy and T the kinetic energy and the various contributions to the solvation energy 18 Keyword ip90 2 in gen section of input file 19 Keyword ip17 2 in gen section of input file Jaguar 5 5 User Manual 131 Chapter 6 Output density matrix If you select this option the density matrix in atomic orbital space is printed out for each iteration For iterations in which Fock matrix updating is performed the change in the density matrix from the previous iteration is printed instead of the density matrix itself The output from the program scf indicates whether Fock matrix updating was performed or not in any particular iteration All J and K matrices AO space The Coulomb
132. useful advice here Also feel free to contact us as described on page 319 For problems with settings you might find the information you need in the online help You can obtain help from any window by clicking its Help button The Help window is displayed with the appropriate topic selected You can also open the Help window using the Help button in the Jaguar panel To choose a topic double click the topic in the Help Topics list or click the topic and then click Select The title of the topic is displayed in the Selection text box and the text of the topic is displayed in the text box above 12 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 st
133. 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 information see the rhosts man page on your machine One further complication can result if you have distinct user names on the local and calcu lation hosts In this case you may get an error like one of the following Jaguar 5 5 User Manual 285 Chapter 12 Troubleshooting Login incorrect remshd Login incorrect rshd xxxx xxxx The remote user login is not correct This problem generally occurs only when the local and calculation hosts 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 calcula tion hostname is replaced by the name of your calculation host See Section 11 1 on page 263 for details on how to construct your own schrodinger hosts file 12 2 Other Problems Some other problems you may encounter are detailed below along with solutions or explanations You cannot read in a particular file as input Make sure you are specifying the right file type in the text box under the directory and file name lists The File type selection alters bo
134. we supply here the correction factors for two and three equivalent sites room temperature 2equivalent sites bases 0 60 acids 0 60 e 3 equivalent sites bases 0 95 acids 0 95 304 Jaguar 5 5 User Manual Chapter 14 The pKa Prediction Module 14 3 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 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 experi ment 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 pro tonated 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 using the current software
135. wfn file which works with RHF ROHF but not UHF a Seetext in this subsection for information on ip151 and information on other options for ip160 The format of the resp file created with the ip172 keyword is as follows The first line contains the number atoms in the molecule and the number of grid points at which the electrostatic potential was evaluated respectively Then the cartesian coordinates of the atoms in bohrs are given Each of the remaining lines contains the electrostatic potential in hartrees the coordinates of the grid point in bohrs at which the electrostatic potential was evaluated and if ip172 3 the grid weights 9 5 21 Output Keywords for Each Iteration The information in Table 9 33 concerns output which can be printed out every SCF itera tion if the keyword is set to 2 Section 6 6 on page 131 describes how to turn on these settings from the GUI 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 itera tion This input file can then be used to restart the calculation To turn off ip152 you must set it to 0 Jaguar 5 5 User Manual 207 Chapter 9 The Jaguar Input File Table 9 33 Effect of Setting Output Keywords for Each Iter
136. while the line for atom O specifies a solvation van der Waals radius of 1 55 for this atom It is not necessary to list information for atoms which are to be treated in the usual 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 218 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File The atom column must be included in every set of atomic input values The corresponding atom identifiers can be either atom labels such as H1 or O in the example above or atom numbers such as 2 for the second atom listed in the zmat input Atom label input is case sensitive e 99 If you do not want to set a value for a given atom you may use a or to indicate that the default value should be used Alternatively you mat leave the values blank for values at the end of the row For instance either the section amp atomic atom mass vdw2 H1 2 00 1 20 H2 2 00 1 20 O 1 55 amp or the section amp atomic atom vdw2 mass H1 1 20 2 00 H2 1 20 2 00 O 4 55 amp has the same result as the first atomic section example listed above 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 e d a
137. window 1 If you were working directly from an input file without using the GUI the geometry input would be in the zmat and zvar sections of the input file 26 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro The Edit menu contains Cut Copy and Paste options to facilitate this task If you already have a geometry you can use the Edit Geometry window to change it To clear the entire geometry input choose Clear from the Edit menu The geometry can be entered in Carte sian X y Z coordinates or in Z matrix format These formats are described below You can also alter the geometry input using the Z matrix menu The Convert to Z matrix and Convert to Cartesians options switch between Z matrix format and Cartesian format The option Assign standard 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 To save or remove your changes or to close the Edit Geometry window use the File menu The Save option stores the changed geometry internally but leaves the window open The changes are not saved to disk until you select OK in the Run window or the Save window The Close option closes
138. window to set any other optimization features that are not unique to transition state searches 19 Keyword igeopt 2 in gen section of input file 88 Jaguar 5 5 User Manual Chapter 5 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 5 1 on page 83 5 3 1 Transition State Search Method The first choice listed in the Transition state search window is the Search method which can be set to standard or QST guided 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 recommend selecting QST guided For a QST guided search you must provide either two geometries corresponding to the reactant and the product or three geometries corresponding to the transition state guess the reactant and the product The distinction between reactant and product is arbitrary for Jaguar Section 5 3 2 on page 90 describes how to specify these structures If you provide reactant and product geometries but not a transition state guess Jaguar generates a transi tion state guess by interpolating between these two structures see Section 5 3 3 on page 90 for more details For the first few steps of a QST guided search the optimizer is restricted to search along the circular curve connecting the reactant transition
139. with tight cutoffs 2 Start with level shift vshift of 6 0 and decrement over 12 itera tions to 0 8 vary level shift during run by raising it when SCF is restarted here when the energy rises by 0 0001 au 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 jksep 0 2J K formed for core when convenient 1 J and K for core are kept separate 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 126 set on or off automatically 1 No Fock matrix updating set iacc 1 if you set noupdat 1 Jaguar 5 5 User Manual 195 Chapter 9 The Jaguar Input File Table 9 27 Integer Keywords for Methods Used in the SCF Convergence Procedures Cont d Keyword Value Description iteravg 0 Do not average density matrices and adjust orbitals accordingly unless istavg keyword requests averaging 20 For iterations whose number is n iteravg 1 where n is an integer revise orbitals so that they correspond to average of density matri ces from preceding and current iterations istavg 0 Do not average density matrices and adjust orbitals accordingly unless iteravg keyword requests averaging 20 For i
140. 0 H1 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat 4 amp 14 5 3 Running pK Calculations To submit a pK job using the GUI follow the instructions for running batch jobs in Section 3 6 on page 38 of this manual Choose pka bat as the batch file and select your pK Jaguar input files as the input files for the batch job 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 either the acid or the base 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 The input file name for the acid is acidfile in the input file name for the base is base file in In this description acid means either the acid or the protonated base and base means the base or the deprotonated acid The number of processors used 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 doe
141. 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 allowed 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 Cartesian coordinates for the optimization rather than generating redundant internal coor dinates and the optimization does not make use of molecular symmetry 3 2 5 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 identifier of atom 1 and the distance between atoms 1 and 2 Identifiers can either be atom Jaguar 5 5 User Manual 29 Chapter 3 Running Jaguar From Maestro 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 place
142. 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 octapole moment no Atomic charges from electrostatic potential Atom O H1 H2 x4 x5 Charge 0 31208 0 63681 0 63681 0 48077 0 48077 sum of atomic charges 0 000000 RMS Error 8 26E 04 hartrees Jaguar 5 5 User Manual 117 Chapter 6 Output 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 a new moment or moments can be calculated from the fitted charges as described in Section 4 6 1 on page 60 The output from ch begins with the moment or moments calculated for the quantum mechanical wavefunction in the format for multipole moment calculations Next the electrostatic potential fitting information is provided as described above Finally the components and totals of the moment or moments recalcu lated using the electrostatic potential charges are reported If you calculate polarizabilities and hyperpolarizabilities with the coupled perturbed HF method the tensor elemen
143. 00000000000E 02 1 09899690000000 S 0 1 0 2 210000000000000E 02 1 00000000000000 P 0 11 10 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 175 55025900 10 00000000 35 05167910 47 49020240 7 90602700 17 22830070 2 33657190 6 06377820 0 77998670 0 72993930 243 36058460 3 00000000 41 57647590 36 28476260 13 26491670 72 93048800 3 67971650 23 84011510 0 97642090 6 01238610 NONIon OUNINMNISDP 1 9 240 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files P D 0 1257 26506820 5 00000000 1 189 62488100 117 44956830 2 54 52477590 423 39867040 2 13 74499550 109 32472970 2 3 68135790 31 37016560 2 0 94611060 7 12418130 KKKK 10 1 2 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 10 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 b
144. 001 in iter0002 in iter0006 inare written by Babel Babel cannot read Maestro formatted files To convert between Maestro format and some other formats a file utility called jagconvert has been provided For conversions between various 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 files BioGraf bgf files XMol xyz files and Maestro mae files It also reads Gaussian9x g9x files and MacroModel dat files but doesn t write them The utility is located in SCHRODINGER utilities The command syntax is as follows jagconvert intype infile outtype outfile where intype is one of ijag ixyz ibgf ig92 or imae and outtype is one of 0jag oxyz obgf or omae 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 11 3 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 appro priate bond lengths scan a potential energy surface or perform a Hartree Fock level geometry
145. 07504316264 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 3 Orbital Energy 0 713206 Occupation For the How option all elements as 8 5 in list ers 1 Orbital Energy 2 Orbital Energy 3 Orbital Energy EN 99466 0 02122 0 00000 0 00395 0 00376 0 00381 0 00037 0 00025 0 00000 0 21055 0 47102 0 00000 0 00141 0 00617 0 00819 0 02205 0 01342 0 14851 0 20 exl 0 555133 Occupation For the How option all elements as e15 6 in table 1 2 3 9 946611E 01 2 105494E 01 Jl 2 2 122377E 02 4 710188E 01 vel 5 1 550432E 03 8 586249E 02 6 4 301783E 03 4 177747E 01 ee 16 4 988566E 06 1 485137E 01 2 4 988566E 06 1 485137E 01 vee 25 2 520402E 04 1 341957E 02 6 8 The Log File 1 000000 Symme
146. 1 input file section 217 218 keywords ertet 172 173 pseudospectral implementation 156 158 SELUTIES ice retener eie 54 56 LMP pairs delocalization of 172 173 217 218 input file section for 172 173 217 218 Jaguar 5 5 User Manual Index input keywords for 172 173 keywords for sse 172 ATMA PFO STAM 25 5 lt assscavssisaceroceciseescepncseosoes 232 Imp2der progtam eee 232 Imp2drp program rrt enentnn 232 lmp2gda program eee 232 lmp2gdb program eee 232 output from sese 110 Local Density Approximation LDA 51 159 dftname values for 174 local h stas orsoni 285 local job directory 39 45 local LMP2 method 55 56 Di 211 key WwOtds 5 remet reis 205 local MP2 method see LMP2 method local LMP2 method Local MP2 window es 54 56 local program localization of orbitals for LMP2 calculations 35 173 keywords 173 200 OPHONS FOT D X 79 log ile eene 25 45 46 136 137 M Tie CHA A program oerte 233 machines LINUX file 292 293 machines LINUX file 291 MacroModel dat files problems reading 286 Maestro customizing settings with schrod inger hos
147. 11 3 on page 275 provides details on batch scripts To run a Jaguar batch job from the Jaguar Batch window you first need a batch script You can create a batch script from the current job settings gen section keywords by choosing Use current job settings from the Script menu You can name the batch script in the Name text box and write it to disk in the current working directory by clicking Write Script A batch script is written to the launch directory using the name in the Name text box when the batch job is launched if you do not explicitly save it To use an existing script choose Use existing script from the Script menu then click Select Script and choose a script in the Select Batch Script window The batch script can be in any of three directories The batch script directory installed with Jaguar identified as BUILTIN SCRIPTS Your own Jaguar batch script directory which can be set in the environment variable JAGUAR SCRIPTS and by default is jaguar scripts The current directory the directory containing the last input file you read in or wrote out or if you have not read or written any files the directory you were in when you started Maestro Jaguar 5 5 User Manual 41 Chapter 3 Running Jaguar From Maestro Select Batch Script Script BUILTIN SCRIPTS TOBS Notes Run the input file s as given l EG This script processes input files Built in scripts Scripts geopt df t I bat g
148. 116 117 118 119 120 121 122 123 124 125 126 127 References 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 S23 269 Head Gordon M Pople J A J Chem Phys 1988 59 5777 Murphy R B Messmer R P J Chem Phys 1993 95 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 114 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 59 52 Culot P Dive G Nguye
149. 2 9 0 4 2 2 dimethylpropanoic 4 5 5 0 0 5 2 furanecarboxylic 3 5 3 2 0 3 cis 2 methylcyclopropanecarboxylic 4 3 5 0 0 7 trans 2 methylcyclopropanecarboxylic 4 5 5 0 0 5 2 methylpropanecarboxylic 4 7 4 6 0 1 cis 3 chlorobut 2 enecarboxylic 3 9 4 1 0 2 trans 3 chlorobut 2 enecarboxylic 3 6 3 9 0 3 3 chloropropanecarboxylic 4 3 4 1 0 2 cis 3 chloropropenecarboxylic 4 0 3 5 0 5 trans 3 chloropropenecarboxylic 3 7 3 8 0 1 3 chloropropynecarboxylic 26 1 9 0 8 3 nitro 2 propanecarboxylic 4 1 2 6 1 5 3 oxopropanecarboxylic 4 9 3 6 1 3 cis 4 chlorobut 3 enecarboxylic 4 3 4 1 0 2 trans 4 chlorobut 3 enecarboxylic 4 2 4 1 0 1 acetic acid 4 0 4 8 0 8 acrylic acid 3 7 4 2 0 5 benzoic acid 3 9 4 2 0 3 butanoic acid 4 5 4 8 0 3 trans cinnamic acid 4 3 4 4 0 1 formic acid 3 2 3 8 0 6 glycolic acid 3 3 3 8 0 5 308 Jaguar 5 5 User Manual Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group Chapter 14 The pKa Prediction Module MOLECULE pKa calc pKa exp Deviation glyoxylic acid 2 0 2 3 0 3 malic acid 3 1 3 5 0 4 malonic acid 3 6 2 9 0 7 oxalic acid 24 1 2 1 2 pentafluoropropanoic acid 0 8 0 4 1 2 propanoic acid 4 4 4 9 0 5 propargylic acid 2 3 1 9 0 4 succinic acid 4 3 4 2 0 1 dl tartaric acid 3 1 3 0 0 1 meso tartaric acid 2 6 3 2 0 6 tartonic acid 25 2 4 0 3 trifluoroacetic acid 0 8 0 2 0 6 THIOLS methylthiol 9 9 10 3 0 4 ethylthiol 10 7 10 6 0 1 2 mercaptoethanol 9 3 9 4 0 1
150. 26 smallest eigenvalue listed in output 102 P P4 GLOBMEMSIZE environment variable 296 parallel execution sess 39 298 frequency jobs 289 jobs that can t be run 289 optimum processor number 298 parallel Jaguar module IBM installation s 296 installing cerent ees 289 Linux installation 291 SGI installation sess 290 partial charge from ESP fit cete 60 partial charges Mulliken 2 4 tiit tees 64 PATH environment variable 282 291 path input file section eee 231 path specifying order of programs input file section for 231 234 PDL program eese rti 233 output from geometry optimizations 116 per iteration output options 131 132 207 208 physical constants and conversion factors keyword for iint 195 pick state ix 10 Pipek Mezey localization 55 79 keywords for sss 173 200 orbital printing eee 133 340 pKa calculation Ab initio 5i ee ee aia 300 conformational flexibility in 303 empirical corrections in 302 equivalent sites in 303 304 geometry optimization in 300 initial geometry iN eee 318 input files for sss 2315 MOMI
151. 3108 zcoor 0 454006 describes the same water coordinates as the previous Cartesian input example If you performed a geometry optimization using this input structure 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 Cartesian input 28 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor Z variables ycoorz0 753108 zcoor 0 454006 is equivalent to the previous Cartesian input example Note that if Cartesian input with variables is used for an optimization Jaguar will perform the optimization using Cartesian coordinates instead of generating redundant internal coordinates and the optimization will not make use of molecular symmetry 3 2 4 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 Carte sian coordinates that should be frozen during a geometry optimization by adding a sign after the coordinate values For example if you add constraints to the zcoor vari ables in the water input example as listed below Oo 0 000000
152. 329 Index for initial guess 76 227 242 in generated GAUSSIAN 9x input file 144 keyword for list in output 204 KEY WOLdS iisasssctiesseesccscciccscssassassassaveavens 193 listed in output eee 102 minimal with GVB 57 polarization functions 770 74 193 238 specifying for GAUSSIAN 92 Input 5 2 e toetiieines 145 206 with ECP in output 123 basis set superposition error 32 54 55 156 Basis Set window sssss 70 74 batch input file example formatene batch jobs jaguar batch command for 275 280 Iemolte oe retener eterne 280 running from Maestro 40 44 BFGS method for Hessian updating input Key word fot eet 182 BIOGRAF bgf and hes files reading hes files format reading files from Maestro bohr units for geometry I pUt estie 164 165 168 229 bond angles treezing all i cn ttr 86 freezing for geometry optimization 32 86 87 166 In Z Inatrix eissis itte ite tive 30 output keyword esse 205 bond dissociation sues 58 141 assignment of GVB pairs for 141 preferred level of treatment of 58 bond lengths freezing all ence ips ech case tece 86 freezing for geometry optimization 32 86 87 166
153. 4 Options 4 9 7 Final Localization of the Orbitals By default the final wavefunction is not localized You can localize the valence orbitals after the wavefunction is computed with either the Boys procedure 46 or the Pipek Mezey procedure 47 If you choose Boys as a Final localization method Jaguar local izes the doubly occupied orbitals by maximizing the term Eo Arie e rlo ar 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 6 7 on page 133 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 local ization 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 7 2 on page 142 for information on restart files and restarting jobs 4 9 8 Symmetry 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 turn the use of symmetry off For information on how to make sure the symmetry of your input struc ture is treated as you expect see Section 3 5 2 on page 37 For some calculations including GVB LMP2 GVB LMP2
154. 42 from electrostatic potential fit 62 keyword for 189 OUTPDUL acierto re t RR E 116 output option eeeeeeernee 125 recalculating from electrostatic potential fitting 62 118 recalculating from Mulliken population analysis 62 64 121 tensors listed in output 116 units keyword Murtagh Sargent method keyword for 182 N Natural Bond Orbital NBO calculations ses 64 121 236 nbo input file section eee eee 236 neighbor ranges seen 244 nice option jaguar run command 270 non local ensity approximation NLDA 159 nude program sssi nete 232 number of iterations for geometry convergence maximum 83 141 181 number of processors determining OpPUMU eea eee herren popa ue 298 numeric updating of Hessian keyword for 182 numerical gradient of energy 83 keywords for s 180 184 output from 112 numerical Hessian printing in freq output 205 numerical methods 78 147 149 cutoff file determination of 253 numerical second derivative of energy 65 66 keywords for 182 184 192 Jaguar 5 5 User Manual O OCBSE convergence scheme TI onee program eeseeeeeee nenne 232 output from 102 103 110 112
155. 47 of the usual Hartree Fock reference wave function a procedure which involves a unitary transformation of the occupied canonical Hartree Fock orbitals This localization procedure which is similar to the localization of bond pairs for the GVB representation of a molecule does not change the reference energy 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 wavefunctions are also available with the local local MP2 method which allows you to treat only some atoms at the LMP2 level while the remaining atoms are treated at the HF level Local local MP2 calculations use the Pipek Mezey localized orbitals that are localized on the specified atom pairs The atomic orbital coefficients for each Pipek Mezey orbital are evaluated and 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
156. 5 Keywords for SCF Methods Many of the keywords that control the SCF calculation can be set from the Methods window as described in Section 4 9 on page 74 The other keyword settings corre sponding to Methods window settings are described in Section 9 5 16 and Section 9 5 17 The two real valued convergence criterion keywords are econv the energy convergence criterion which dictates the maximum difference in energy between one SCF iteration and the next for convergence to be assumed and dconv the criterion for the root mean square Jaguar 5 5 User Manual 193 Chapter 9 The Jaguar Input File change in density matrix elements The default value of econv is normally 5 0 x 10 Hartrees However for polarizability or hyperpolarizability calculations econv is 1 0 x 10 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 0 x 106 the calculation is considered to have converged By default calculations use the DIIS or GVB DIIS convergence scheme which gener ates 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 which has a default value of 10 sets the maximum number of Fock matrices that are used for this scheme during any iteration The keyword stdiis gives an error
157. 588607997 6 8E 04 6 6E 03 etot 2 Ys Y M 76 03615425936 2 7E 04 1 9E 04 1 8E 03 etot 3 Y N 6 M 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 solvent 0 02160511215 E Total one electron terms 123 39806065860 F Electron nuclear 199 21812919134 G Electron solvent 0 03443064237 H Kinetic AW e e eS 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 A1 1 34624 A1 0 71287 B2 0 57176 A1 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 en
158. 82 3pd D95V H Li Ne WEN analytic 6 83 D95 H Li Ne EE H Li C F Si Cl pseu 6 83 Al Cl dospectral others analytic MSV H Ru Pd Xe analytic 5 84 cc pVDZ H He B Ne H C F Si Cl pseudospec 5 85 88 Al Ar tral others analytic analytic cc pVDZ d H He B Ne H C F Si Cl pseudospec 5 85 88 without d Al Ar tral others analytic functions analytic cc pVTZ H Ar Ca Ga H C F Si Cl pseudospec 5 85 88 Kr tral others analytic cc pVTZ f H Ar Ca Ga H C Ne Si Ar pseudospec 5 85 88 without f Kr tral others analytic functions cc pVQZ g H F Na Ar H C O pseudospectral 5 85 without g Ca Ga Kr others analytic ana functions lytic MIDI H C F P CI pseudospectral 5 89 TZV H Kr Fay analytic 5 90 TZV f Sc Zn analytic 5 90 The other available basis sets which are listed in Table 4 4 include effective core poten tials ECPs The names of eight of these basis sets begin with LA to indicate they were developed 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 LAV 1 indicates that the basis set has been fully contracted to form a minimal basis set LAV2 that the last Gaussian has been uncon
159. 9 14 Values of i in idft Where idft ijklm i in idft Hybrid Method i 0 none i l half amp half functional coefficients are all 0 5 i 2 Becke 3 parameter parameters from ref 27 i 3 Becke 1998 B98 i 4 Schmider and Becke 1998 SB98 i 5 Becke 1997 reparametrized B97 1 If the value of i in idft is 1 or 2 the functionals given by j k L and m are combined using coefficients determined by the appropriate hybrid method as indicated in Table 9 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 For Becke 3 parameter hybrids you need to specify a Slater or Xo local exchange func tional 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 3 parameter hybrid you must list a purely local correlation functional 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 coeffi cients of the ex
160. 91 geometry optimization 179 TG AEE EA TTS 210 ON B A TS 170 ittial guess ceto RUE 198 lewis dot structure 170 localization 2 onis 200 memory usage eeeeeeeeeeeeeneene 212 orbital output esee 208 properties iiteiateiecedisiseseeittiens 188 SCF iteration essere 207 SCP method ette 195 Solyation iride isses sitis 187 standard output 204 transition state sese 179 killig JOBS roii 271 L launch host sssss 23 283 284 LDA see Local Density Approximation least squares operator Q description of 147 148 level shifting of Hessian keyword for 183 of SCF orbital energies 78 Lewis dot structure keywords for sss 170 171 lewislesse enn 237 setting GVB pairs from 170 171 setting van der Waals radii from 113 187 lewis file description and format 253 262 specifying in input file 161 Linear Synchronous Transit LST methods see QST guided transition state searches LMP calculations setting up 55 Imp2 input file section 217 LMP2 method 54 56 156 158 counterpoise corrections 32 DTI MS 211 grid used for sss 21
161. 9354 H1 2 21 39 1d 15 2 8253944 0 2347270 0 3645712 H1 3 A 0 b 15 0 6401217 0 8137573 0 4150514 H1 4 X orn X 16 0 1612778 1 0000000 0 1813806 H1 5 t 0 2 17 1 1000000 1 0000000 1 6057611 H2 1 3 70 cT 20 18 7311370 0 0334946 0 2149354 H2 2 L 9 41 20 2 8253944 0 2347270 0 3645712 H2 3 aa O o el 20 0 6401217 078137573 0 4150514 H2 4 X oI 21 0 1612778 1 0000000 0 1813806 H2 5 T 0 2 22 1 1000000 1 0000000 1 6057611 The second table an example of which follows below shows information for the basis functions themselves the Cartesian components of each shell For instance the entries X Y and Z for the tenth shell correspond to p p 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 normalization can be different for different compo nents The rmfac values provide the ratio of the normalization to that of the first compo nent listed which is the x component Gaussian Functions Normalized coefficients s Teck e y Iep f atom 1 e n Zz rcoef rmfac rcoef rmfac O 1 sS 1 5484 671660 0 831724 1 000000 0 831724 Oo 2 S 1 825 234946 1 530816 1 000000 1 530816 Oo 3 78 1 188 046958 2 477149 1 000000 2 477149 Oo 4 S 1 52 964500 3 256281 1 000000 3 256281 Oo Br 2S 1 16 897570 2 792893 1 000000 2 792893 O 6 S 1 5 799635 0 954938 1 000000 0 954938 Oo TAES 2 15 539616 0 617934 1 000000 0 617934 Oo 8 S 2 3 599934 0
162. AERES 141 7 1 4 Electrostatic Potential Charge Fitting 5 ient 142 7 2 Restarting Jobs and Using Previous Results eee 142 vi Jaguar 5 5 User Manual Contents 7 5 Suggestions for GAUSSIAN Ox Users inset treesteec tre reete e eed reed 143 7 3 1 Generating GAUSSIAN 9x Input Files With Jaguar 143 7 3 1 1 Making Input Files for GVB Calculations 144 7 3 1 2 Other Jaguar Options for the 992 File sess 144 7 3 2 Getting Basis Sets or Orbitals for GAUSSIAN 9X esee 145 7 3 3 Using GAUSSIAN 9x Files as Jaguar Input eese 145 rcu M cy Prem 147 8 1 The Pseudospectral Method etd RR he tugben 147 8 2 Pseudospectral Implementation of the GVB Method 149 8 3 GVB ECI WayefulctQDs 5 3 10 ER eite tre pert HN EE EE ERE URE 153 8 4 Pseudospectral Local MP2 Iechauques etre rtr rrt 156 8 5 Density Pugschonal TB6OLDy tetris 159 Chapter 9 The Jaguar Input File eee cee ecce e eene eene erento sta uno 161 9 1 General Description of the Input File essiri a 161 9 1 1 Sections Describing the Molecule and Calculation 162 9 2 The zmat zmat2 and zmat3 Sections 164 9 3 The zvar zvar2 and zvar3 Sections esee 166 9 4 The coord and connect Sections eese 166 9
163. AL P OW CP QN IZ Ovr A 6 S 8 LE crt PUL OTT OCT colt OCT SCE LTE SUT OFT LUE LUT SUL col CET vVT YLT EOT TH O9t d St 9S vt SV ECOD Ct D IEJUZ Ot nD 6C IN 8T OD LTA 9c UIN SCHO CJA ETIL CCS ITED OTA 6l 860 660 TOT 90 T TTT 8IT 9 I PST IV 8I ID LIS 9l d SI IS TI IV el SIN CL N II ILO TLO ELO SLO LDO C80 060 CI N Old 60O 8N LID 9 S ed HI 60 TEO PH T H I 876 uouoog ui paquaosoap sv pf mdui uv fo uo1j228 21140JD 21 u1 S2uiJ2s AOD Suivi Kq pa42j p IG UDI s8uijas snippa 2sau c fo anjpa ynvfap 0 ynm p4oaay si 2DfA02 2424 PVA juo paoo 41241 fo UNS AY SAW 2DfAOO UDY SSI 1421 u2204 2q 22uDIsip 211 fi papuoq SWIOJD OM s4apisuoo ANSDS KXj 012u22 swoly uaamjag spuog sp yong uoi2v42 ju fo sj242 210njva 01 pass su41s8uy U1 npuyx 1u2 0407 FF 6 2 qUI Jaguar 5 5 User Manual 224 Chapter 9 The Jaguar Input File counterpoise input In the atomic section counterpoise atoms are indicated by using an entry of n in the column entitled charge see Table 9 45 Also note that any other word or letter such as the Y entries that may appear in restart files indicates that the grid dealiasing function or charged particles for that atom are included the usual default for the grid daf and charge keywords Table 9 45 Keywords for Listing Basis Grid Dealiasing Function and Charge Information for Individual Atoms in an atomic Section
164. 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 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 command 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 12 1 5 on page 285 Jaguar 5 5 User Manual 283 Chapter 12 Troubleshooting If you have problems running the xauth command described in the above paragraph an alternative 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 recommended 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 uncomm
165. B S JOB 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 11 3 5 Running jaguar batch 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 Jaguar 5 5 User Manual 279 Chapter 11 Running Jobs The jaguar command options REL VER HOST USER WAIT and PROCS described in Table 11 3 and Table 11 4 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 11 8
166. BO 6 where the GVB configuration interaction CI coefficients C and C satisfy the following equations C 14S PE _ s p 7a Cpu 0785 2 pe Che t Cpu 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 function This energy is given by the equation 150 Jaguar 5 5 User Manual Chapter 8 Theory 2N vb 2N 2 2CRhyyt Gud SEI 8 gvb 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 Npasis Wi M ip 9 i The terms hpp Jy and Ky are defined by N basis huy Wl Cape jul oes Npasis j gt Ciut y pA N basis Ja HHI ul Y euet 10b N basis N basis 2 7 D CiyC jy gt Coy Ci GJ KL kI N pasis Ku AVIV K Y eue Ky 10c N basis N basis A c WEN cy ey Gk jD ij and the quantities a and b obey the following rules 0 11a ay 7 0 by CQC 11b for u and v in the same pair u z v and Jaguar 5 5 User Manual 151 Chapter 8 Theory Dy 27 2 ay 2C C buy C C 11c for u 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 V 2 S v v Fy Cyhyt 5 ay Jj
167. COTING iot eicit ea 317 multiple protonation sites in 303 305 TUNING 2 5 gc dne piede 316 single point energies in 301 solvation free energy in 301 juro S I 300 pKa prediction module 1nstallitig acentos 315 introduction oci 299 parameterized functional groups 306 results 305 plot data generating 79 214 234 plot input file section 234 POE Parallel Operating Environment options automatically set version required T point charges input file section for 229 pointch input file section 229 Poisson Boltzmann equations 59 Poisson Boltzmann solver 58 60 output from esee 115 polar ptogram eret rte 232 polarizability keywords for s 189 190 options for essere 62 63 POSE PLO STAM c csv cesessnussrevervesnessenesansas 233 output from sees 113 post SCF DFT calculations 50 potential energy surface scan 93 94 potential electrostatic plot ng eth 234 236 Powell update method keyword 182 PES program nan output from Preferences panel pressure for thermochemical calculations keyword for eere 192 option for Jaguar 5 5 User Manual probe radius of solvent
168. 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 devel oped and tested at Schr dinger Inc Cundari T R Stevens W J J Chem Phys 1993 98 5555 Hurley M Pacios L E Christiansen P A Ross R B Ermler W C J Chem Phys 1986 84 6840 Lajohn L Christiansen P A Ross R B Atashroo T Ermler W C J Chem Phys 1987 87 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 Theor Chem 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 5 5 User Manual 105 106 107 108 109 110 111 112 113 114 115
169. 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 without performing SCF or other later calculations lewstr 0 Print all Lewis dot structures if lewdot 1 or 1 20 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 2 Select heteroatom GVB pairs only according to igvbsel and Lewis dot structure lewstr heteroatom pairs are all pairs whose atoms are different elements except for C H pairs mm 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 Mu O t A U N Select sigma pi second pi and lone GVB pairs default when igvball gt 0 The values for igvbsel are easier to remember if you associate the number 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 Jaguar 5 5 User Manual 171 Chapter 9 The Jaguar Inpu
170. Electronic Structure Calculations on Large Mole cules 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 W A III A generalized direct inversion in the iterative subspace approach for generalized valence bond wave functions J Chem Phys 1994 100 1226 Murphy R B Friesner R A Ringnalda M N Goddard W A III Pseudospec tral Contracted Configuration Interaction From a Generalized Valence Bond Refer ence J Chem Phys 1994 101 2986 Jaguar 5 5 User Manual 321 References 13 14 15 16 17 18 19 20 2 22 23 24 322 Greeley B H Russo T V Mainz D T Friesner R A Langlois J M Goddard W A III Donnelly R E Jr Ringnalda M N New Pseudospectral Algorithms for Electronic Structure Calculations Length Scale Separation and Analytical Two Electron Integral Corrections J Chem Phys 1994 101 4028 Langlois J M Yamasaki T Muller R P Goddard W A Rule Based Trial Wavefunctions 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 Ringnalda M Goddard W A III Honig B Accurate First Principles Calculation of Molecular Charge Distributions and So
171. GA 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 local and nonlocal correlation functional 178 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 9 5 8 CIS Keywords The configuration interaction singles CIS method can be used after a closed shell Hartree Fock calculation to generate information on excited states The output includes energies oscillator strengths and transition dipole moments for excitations from the ground state The keywords used to control the CIS calculation are listed in Table 9 16 You should not normally need to set nrestart because the program determines how many iterations it can do with the amount of memory available Table 9 16 Keywords for CIS Calculations Keyword Value Description icis 0 Do not do a CIS calculation 1 Do a CIS 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 CI 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 CI diagonalization iterations before restarting 0 Determine number of CI diagonalization iterations before restart ing a
172. IAN 9x run guess cards If you have chosen to do an initial guess only calcula tion as described above the initial guess is generated from Jaguar s GVB initial guess routine Otherwise the initial guess provided in the 992 file is the final wavefunction resulting from the Jaguar SCF calculation performed starting from the GVB initial guess 7 3 1 2 Other Jaguar Options for the 992 File You can use a Jaguar input file to run a Jaguar job which generates a g92 file See Chapter 9 for a description of input files Selecting the Gaussian 92 input deck g92 output option described above corresponds to setting the output keyword ip160 to 2 in the gen section of the input file 144 Jaguar 5 5 User Manual Chapter 7 Tips and Suggestions You can create or edit Jaguar input files by hand making keyword settings corresponding to all of the relevant options described above see Chapter 9 for details If you want you can make some of the desired settings in the GUI use the Save window to save a Jaguar input file and edit it by hand later to set other keywords You can generate additional information for the g92 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 g92 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
173. Jaguar 5 5 User Manual Copyright 2003 Schr dinger L L C All rights reserved Schr dinger FirstDiscovery Glide Impact Jaguar Liaison LigPrep Maestro Prime QSite and QikProp are trademarks of Schr dinger L L C MacroModel is a registered trademark of Schr dinger L L C 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 October 2003 Contents Chapter 1 IntrOQUCUlOli 5222 e eee eee eee te eto aera n neve essere eto ee tane vna eire reser ue 1 1 1 Conventions Used in This Mantual i eir RR Ree repere inet 2 12 gt Citing Jaguar in Publicatiagis 5 eite iter er be Pete te ER 3 Chapter 2 The Maestro Graphical User Interface eres 5 2 1 Star np MaesttO iie eine t rp hrec ome Dude ebur REOS RS DR g aed 5 2 2 The Maestro Main WIDOOW io rere etre eme t tb rir cheer 7 2 2 Maestro Projects eicere erirerer eerte Lite ee pet eee in ere d Eee ERR YI Pe PE ee rue ER ERE Fe GESSEREN 7 24 Building a SUTIN uc ceret eere eem terer re iieri e eter ied RE Eee eee pon 9 2 9 Atom Selecbloti ouo eene e eem EEEE EEEE A E AE EEE ARE aasi 10 2 6 Toolbar CoO Eanan aE R R 11 2 1 Monse Futctions oid rete ier t i Ee ERES E Rn 14 2 7 1 Mouse Functions in the Workspace esee nre 14 2 7 2 Mouse Functions in the Project Facility r
174. Job window which is accessible by clicking on the Edit Input 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 multiplicity 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 frag ment The third entry under the heading multip should be the spin multiplicity of the fragment If C1 is in one ring of ferrocene and C2 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 C1 1 1 C2 1 1 amp 140 Jaguar 5 5 User Manual Chapter 7 Tips and Suggestions Fragments with no formal charge and singlet spin water for example do not need to be listed in the atomic section because Jaguar 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 molchg
175. N The definitions of polarizabilities first hyperpo larizabilites B and second hyperpolarizabilities y are 2 3 4 d E dE dE oi TF dF Bike qp dF dF i 7 Ge dF 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 f for closed shell wave functions The finite field methods corresponding to ipolar gt 0 differ in the data they use for numer ical 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 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 calculations using fields of aE and aE in the x y and z directions where a is some constant Similarly 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 directions 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 4 0 Similarly for any polarizability calculation the Methods keywo
176. Output settings are turned on is explained Finally the log file is described Chapter 7 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 incorporate results from previous runs and some tips on using both Jaguar and GAUSSIAN 92 Chapter 8 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 GVB RCI and local MP2 techniques and a brief description of density functional theory Jaguar 5 5 User Manual 1 Chapter 1 Introduction Chapter 9 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 10 describes other Jaguar files that are necessary for calculations You may skip Chapter 9 and Chapter 10 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 11 provides information on configuring hosts the environment and the Schr dinger software to run Jaguar submitting jobs from the command line and running multiple Jaguar jobs using batch scripts Chapter 12 contains troubleshooting hints concerning various problems you might encounter especially when first setting up Jaguar on your system Chapter 13 c
177. Shortcut Keys in the Maestro GUI Continued Keys Action Equivalent GUI Operation In the Project Table Panel ALT A Select all entries Select gt Select All ALT F Fix entry in Workspace Selection gt Fix In Workspace ALT I Show import panel Table gt Import Structures ALT N Include only selected entries Selection gt Include Only These In Workspace ALT U Unselect all entries Select gt Unselect All ALT X Exclude selected entries Selection gt Exclude From Workspace In the Plot Panel ALT A Select all Plot gt Select All ALT U Unselect all Plot gt Unselect All ALT P Show plot settings panel Settings gt Plot Settings 2 9 Undoing an Operation To undo a single operation click the Undo icon in the toolbar choose Undo from the Edit menu or use the key combination ALT Z The word Undo in the menu is followed by some text that describes the operation or operations to undo Not all operations can be undone global rotations and translations are not undoable operations for example However you can use the Save view and Restore view buttons in the toolbar to save a molecular orientation and restore it at a later time If you know in advance that you might want to undo a series of operations you can start an undo block by selecting Begin Undo Block from the Edit menu When you have completed the group of operations you want to undo end the block by selecting End Undo Block from the Edit menu Then to undo the operatio
178. The functionals available from the option menu are described below Functionals with local exchange only HFS gt Slater local exchange functional 29 e Xalpha Xo local exchange functional 29 Functionals with local exchange and local correlation SVWN Slater local exchange functional 29 Vosko Wilk Nusair VWN local cor relation functional 30 e SVWNS Slater local exchange functional 29 Vosko Wilk Nusair 5 VWNS local correlation functional 30 Functionals with local and nonlocal exchange and correlation BLYP Exchange Slater local functional 29 Becke 1988 nonlocal gradient correc tion 32 correlation Lee Yang Parr local and nonlocal functionals 33 e BPW91 Exchange Slater local functional 29 Becke 1988 nonlocal gradient cor rection 32 correlation Perdew Wang 1991 GGA II local and nonlocal functionals 31 e BP86 Exchange Slater local functional 29 Becke 1988 non local gradient cor rection 32 correlation Perdew Zunger 1981 local functional 34 Perdew 1986 gradient correction functional 35 Keyword dftname hfs in gen section of input file Keyword dftname xalpha in gen section of input file Keyword dftname svwn in gen section of input file Keyword dftname svwn5 in gen section of input file 9 Keyword dftname blyp in gen section of input file 10 Keyword dftname bpw91 in gen section of input file 11 Keyword dftname bp86 in gen section of input fil
179. U H or G in the table below p ow 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 6 3 11 Basis Set If your calculation uses a basis set that includes effective core potentials the output lists the number of atoms treated with effective core potentials 6 3 12 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 4 8 on page 70 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 o
180. VB orbitals the number of GVB and RCI pairs the numbers of occupied and virtual orbitals the numbers of Coulomb and exchange Hamiltonians and the multiplicity Next the total energy of the 108 Jaguar 5 5 User Manual Chapter 6 Output GVB wavefunction which was obtained from the SCF procedure earlier is listed and broken down into a nuclear repulsion term and terms from the core which is treated with Hartree Fock methods the GVB pairs and the open shell contribution If you specified GVB pairs that were not also RCI pairs a non zero value is listed for the non RCI GVB pair energy The number of RCI spatial configurations and the number of RCI configura tion state functions follow Each RCI configuration state function is the product of a contracted spatial function and a spin function the number of these functions indicates the size of the RCI expansion The rci output lists the RCI initial guess energy next followed by the converged total RCI energy For small cases the initial guess and the converged energy may agree exactly since the RCI coefficients are obtained by one diagonalization of a small matrix For larger cases the output includes the results of the iterative diagonalization 6 3 5 Geometry or Transition State Optimization HF GVB DFT and LMP2 The output format description for optimizations in this subsection applies to calculations of either minimum energy structures or transition states Although the Hessian
181. VTZ basis sets we find a scaling N with system size The physical idea behind the LMP2 method is that if the molecular orbitals are trans formed so that they are localized on bonds or electron pairs correlation among the occu pied 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 local ized orbitals can be generated by any unitary transformation of the canonical orbitals For 156 Jaguar 5 5 User Manual Chapter 8 Theory LMP2 we use Boys localized 46 orbitals for which the term Z jKodrle o nde 2 i maximized The local virtual space for each atom is defined by orthogonalizing its atomic basis functions against the localized molecular orbitals The correlating orbitals included in the local virtual space are thus mostly near the atom itself but because of the orthogo nalization procedure they are not particularly well localized The Jaguar LMP2 program uses Pulay s method 43 44 45 to expand the first order wavefunction correction 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 yp _ yy 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 E 2 _ Tj K FC S S8C F 19 ij s
182. 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 cal culations see iconv 4 3 OCBSE convergence 194 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 27 Integer Keywords for Methods Used in the SCF Convergence Procedures Cont d Keyword Value Description 4 GVB DIIS convergence default for GVB open shell singlet calcu lations and calculations whose initial guess is obtained from H maxit 0 Calculate energy but do not update wavefunction i e do only one iteration gt 0 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 2 Accurate mixed grid types accurate cutoffs default choice for transition 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 itera tions to 0 8 keep number of canonical orbitals fixed during optimi zation run at ultrafine accuracy level and
183. When the groups are close together there are some scientific issues about the accuracy of results for multiply protonated states This will become clearer as more test cases are run In the next release we intend to treat case 3 inside the program With the present software you must run two separate pK jobs each of which handles two of the four protonation states and build the titration curve by hand 14 4 Training Set Results Table 14 1 presents a summary of the results for the functional groups that we have param eterized including the number of cases studied average deviation from experiment and maximum deviation A listing of the results for the individual test cases comparing exper imental and calculated pK values can be found in Table 14 2 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 3 and maximum error of 0 9 that we observe The carboxylic acids include some examples with polyfunctional groups and significant flexibility 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 Nevertheless the errors are quite respectable The largest error for alcohols comes from t butanol wi
184. Wilk Nusair 5 local correlation pl 300 Perdew Zunger 1981 local correlation ps6 1300 Perdew Zunger 1981 local correlation Perdew 1986 non local gradient correction pw91 4400 Perdew Wang GGA II 1991 local and nonlocal correla tion lyp 2000 Lee Yang Parr local and nonlocal correlation If you choose to use the idft keyword you can construct a combined functional from the available 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 7 100 k 10 I m or idft ijkIm where the values of j k l 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 9 10 through Table 9 13 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 correla tion functional 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 functional which contains local and non local terms you may not specify a local correlation functional i e if j 2 k must be 0 unless you are using the Becke 3 parameter hybrid method as described below Table 9 10 Values of m i
185. X Q Hoi H20 lig 13 im D H14 ligand j Hoi H20 lig 14 im IR H15 ligand Qi Hoi H20 lig 15 imi D H16 ligand Qi HoiH20 lig 18 imp H01 H20 lig i7 imp H01 H20 lig 18 imp UD 4 2 V E H1 ligand 18 Hi8 ligand 19 H19 ligand 20 21 DX DX DX DI IL 4 l MA UD H20 ligand IFTE protein Q 5 NINNA ORY Save Workspace Changes Mark Belected Entries Selected Included Excluded Fixed or locked entries entry entry entry Figure 2 2 The Project Table panel You can choose the entries to include in the Workspace using the In column of the Project Table panel To include a single entry and exclude all other entries click in the In column for that entry To include a range of entries hold down SHIFT and click the first and last entries To choose individual entries for inclusion or for exclusion if they are already included hold down CTRL and click the entries Including an entry causes any structures associated with that entry to be displayed in the Workspace You can also fix or lock entries in the Workspace by selecting the entries and choosing Selection gt Fix in Work space or pressing ALT F A padlock icon is displayed in the In column to denote fixed entries To remove a fixed entry exclude it from the Workspace Fixed entries are not affected by the inclusion or exclusion of other entries There are shortcuts for sele
186. a regular lattice of grid points 56 by choosing rectangular from the ESP grid type option menu You can then set the spacing in bohr between points in this lattice in the Rect grid spacing box 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 57 van der Waals radii for hydrogen and for carbon through argon and universal force field 54 van der Waals radii for all other elements These radii are listed in Table 9 42 The radius settings can be altered by making vdw settings in the atomic section of an input file as described in Section 9 8 on page 218 You can also print out the values of the electrostatic potential at grid points whose loca tions you specify See Section 9 5 12 on page 188 4 6 2 Multipole Moments Jaguar can compute multipole moments through hexadecapole for HF GVB or DFT wavefunctions and can compute dipole moments for LMP2 wavefunctions 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 If you select one of the higher order moments all moments of lower order are also calcu lated If atomic charges are computed either by fitting of the electrostatic potential 55 56 as described above or by Mulliken population analysis 58
187. act 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 respec tively If the Lee Yang Parr functional is used in a Becke 3 parameter hybrid its coeffi cient 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 contri butions of the exact exchange and the exchange functionals while the keywords xcorln and xcornln control the contributions of the correlation functionals as listed in Table 9 15 For example with the keyword settings idft 1 xhf 0 332 xexll1 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 Finally if you want to evaluate the energy of the final post SCF wavefunction using a particular functional 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 for idft If jdft 1 you can set up a customized functional using Jaguar 5 5 User Manual 177 Chapter 9 The Jaguar Input File the keywords yhf yexl1 yexl9 yexnln ycorln and ycornln which correspond to the keywords in Table 9 15 e g xexl1 If you do a post SCF DFT
188. adison WI 2001 Baker J Jarzecki A A Pulay P J Phys Chem A 1998 102 1412 Scott A P Radom L J Phys Chem 1996 100 16502 Hehre W J Stewart R F Pople J A J Chem Phys 1969 51 2657 Jaguar 5 5 User Manual 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 References Hehre W J Ditchfield R Stewart R F 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 Gordon M S Binkley J S Pople J A Pietro W J 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 Ch
189. air VWN local functional 30 Lee Yang Parr local and nonlocal functional 33 b3pw91 Exchange exact HF Slater local functional 29 Becke 1988 non local gra dient correction 32 correlation Perdew Wang 1991 local and GGA II non local functional 31 b3p86 Exchange exact HF Slater local exchange functional 29 Becke 1988 non local gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 and Perdew 1986 nonlocal gradient correction 35 bhandh 50 exact HF exchange 50 Slater local exchange functional 29 bhandhlyp Exchange 50 exact HF exchange 50 Slater local exchange functional 29 correlation Lee Yang Parr local and nonlocal functional 33 b97 1 Reparametrization of Becke s 1997 hybrid functional 36 by Hamprecht Cohen Tozer and Handy 39 598 Becke s 1998 hybrid functional including the Laplacian of the density and kinetic energy density terms as well as gradient terms 37 sb98 Schmider and Becke reparametrization of Becke s 1998 functional 38 174 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 9 Functional Name Strings for Construction of the dftname Keyword Name String idft Value Functional Description S 1 Slater local exchange xa 9 XQ local exchange b 11 Becke 1988 nonlocal exchange Slater local exchange pw 41 Perdew Wang 1991 GGA II nonlocal exchange Slater local exchange vwn 100 Vosko Wilk Nusair local correlation vwn5 200 Vosko
190. al forces or frequencies default is 0 05 Distance of LST transition state initial guess between reactant and product geometries Default is 0 5 range is 0 0 to 1 0 trust Initial trust radius in atomic units bohr and or radians if norm of proposed displacements exceeds trust radius step size is reduced as described by itrcut trust default is 0 3 except for solvated cases or transition state optimizations when it is 0 1 tradmx Maximum trust radius allowed during optimization for itradj gt 0 see trust information tradmx default is 0 3 except for solvated cases when it is 0 1 tradmn Minimum trust radius allowed during optimization for itradj gt 0 see trust information tradmn default is 0 01 tremx Trust radius reduction criterion if relative error between actual and predicted energy changes is more than tremx and itradj gt 0 trust radius is reduced default is 0 25 trgmx 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 trgmx 0 0 by default treok 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 Scale factor for trust radius adjustment default is 2 0 used only when itradj 2 a Convergence criteria are shown in
191. al mode 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 GVB RCI and GVB LMP2 jobs CPHF hyper polarizability jobs Jobs with more processors than atoms e pK jobs jobs that use the Jaguar batch facility 13 1 Installing Parallel Jaguar Parallel Jaguar is currently available for the SGI Linux and IBM 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 instructions are given in the Schr dinger Product Installa tion 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 computer 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 Jaguar 5 5 User Manual 289 Chapter 13 Parallel Jaguar queuing software an entry must be included for each node and the value of processors for each node should be the total number of processors available in the c
192. al number orbnum which is 0005 for the fifth orbital for instance The orbital file names are of the form j obname_aorbnumMO p1t for instance the tenth orbital from the job h2o would be written to the file h20 40010MO plt A plt file always 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 described by the plot section The first line gives the value at the origin next the values along the vector described by extentz are given The next values correspond to the grid points given by extentz but also displaced from the origin along extenty The loop over the points along extenty continues and the outer loop generating points for displace ments along extentx for the above square grids provides the rest of the points in the file The generation of plot data is incompatible with NBO calculations You must run NBO calculations in a separate job 9 18 NBO 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 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 See the NBO documentation for more details on NBO input and output Jaguar s interface to NBO 5 0 does not sup
193. all jobs described below them unless a later line of the same type replaces them Any TEMP 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 rede fines options already in the options list The syntax for the options set by OPTIONS direc tives is described later and summarized in Table 11 7 Table 11 6 Batch Input File Directives Directive Action EXEC directory SCRATCH directory TMPDIR directory WORKDIR directory files FLAGS options OPTIONS options OUTFILES files ERRORS IGNORE PURGE_JOBDB EXIT Set the directory for the Jaguar executable This directory can be any directory listed by jaguar LIST 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 directory and use it as the working directory for input and output Copy the specified files into the 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 subse quent lines
194. allation directory You can set this variable by entering the following command at a shell prompt csh tesh setenv SCHRODINGER installation directory sh bash ksh export SCHRODINGER installation directory You might also need to set the DISPLAY environment variable if it is not set automatically when you log in To determine if you need to set this variable enter the command echo DISPLAY If the response is a blank line set the variable by entering the appropriate version of the following command csh tesh setenv DISPLAY display machine name 0 0 sh bash ksh export DISPLAY display machine name 0 0 After you set the SCHRODINGER and DISPLAY environment variables you can launch Maestro using the command SSCHRODINGER maestro Jaguar 5 5 User Manual 5 Chapter 2 The Maestro Graphical User Interface If the SSCHRODINGER directory has been added to your path you can simply enter the command maestro Options for this command are given in the Maestro User Manual The directory you were in when you launched Maestro is the current working directory and all data files are written to and read from this directory unless otherwise specified see Section 2 11 on page 18 You can change directories by entering the following command in the main window s command input area cd directory name where directory name is either a full path or a relative path Title bar Auto Help text area Main
195. als which are listed in Table 9 9 The corresponding values of idft are listed along with the functional name strings For example dftname bp86 specifies the BP86 func tional and is a combination of b for exchange and p86 for correlation Jaguar 5 5 User Manual 173 Chapter 9 The Jaguar Input File Table 9 8 Standard Functional Names for the dftname Keyword Name Description hfs Slater local exchange functional 29 xalpha Xa local exchange functional 29 hfb Slater local exchange functional 29 Becke 1988 non local gradient correc tion to exchange 32 hfpw Slater local exchange functional 29 Perdew Wang 1991 GGA II nonlocal exchange 31 bp86 vwn5 Exchange Slater local functional 29 Becke 1988 non local gradient correc tion 32 correlation Vosko Wilk Nusair VWN local functional 30 Per dew 1986 gradient correction functional 35 pwp91 Exchange Slater local functional 29 Perdew Wang 1991 gradient correc tion functional 31 correlation Perdew Wang 1991 GGA II local and non local functionals 31 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 40 pbe Perdew Burke Ernzerhof local and nonlocal exchange and correlation func tional 41 b3lyp Exchange exact HF Slater local functional 29 Becke 1988 nonlocal gradi ent correction 32 correlation Vosko Wilk Nus
196. ame box in either the Run window or the Jaguar panel If you did not read in the geometry from a file the job name Scratch is supplied Any text entered in the box marked Comment appears in the input and output files for the job If you symmetrize the molecule a procedure described in Section 3 5 2 on page 37 the comment contains text noting that the geometry was symmetrized to a certain point group You can enter other text describing the job if you like The comment cannot contain the characters or amp The comment appears in the input file immediately above any keyword settings corresponding to later selections and in the output file under the heading Input file comments By default all temporary files and directories are deleted when the job finishes after the output file restart file which is described in Section 7 2 on page 142 and other useful files are copied back to the local job directory If you want to save the binary files gener ated in the temporary directory s job subdirectory and used during the run use the Cleanup option menu Note however that these files are often large and should be saved only if necessary and any files in the temporary directory may be deleted automatically if your site has automatic purging of scratch disks When you are satisfied with the run time settings start the job by clicking RUN You can then check the current status of the job from the Monitor panel You can close the Monitor panel b
197. and exchange matrices in atomic orbital space can be printed out for each iteration by selecting this option However by default the calculation will be performed by combining these matrices in the form 2J K and they may not be properly separated here if this is the case In order to print out the true J and K matrices you must insure that the Core J and K option in the Methods window whose button is found in the main window specifies that the matrices be kept separate For GVB DFT LMP2 and GVB LMP2 calculations the J and K matrices are kept separate by default Since J and K are symmetric matrices the elements of the upper triangles are not printed Fock matrix in AO HF or MO GVB space The Fock matrix in atomic orbital space for HF or DFT calculations or molecular orbital space for GVB calculations can be printed by turning this option on This information is only printed for iterations where the Fock matrix is not updated Because the Fock matrix is symmetric the elements of the upper triangle are not printed Fock matrix in CO space The Fock matrix in canonical orbital space can be printed by turning this option on Because the Fock matrix is symmetric the elements of the upper triangle are not printed GVB data f a b ci coefficients etc You may print out GVB data for the initial guess and the GVB initial guess by selecting this option 20 Keyword ip110 2 in gen section of input file 21
198. and generally increases computational costs by a factor of two to three e f the calculation is a DFT job use finer DFT grids You can make this setting from the Grid density option menu in the DFT window This setting also increases the com putational cost For transition metal containing systems particularly organometallics you can often obtain superior results by improving the initial guess wavefunction 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 collection 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 transi tion metal atoms and non transition metal atoms were broken Typically the system is broken into ligand fragments and transition metal fragments or adsorbate fragments and cluster fragments For example for ferrocene the iron atom is one fragment and the two cyclopentadienyl 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
199. andard 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 cshro or other startup files in your home directory If you can start Maestro but you have problems submitting jobs skip to Section 12 1 4 on page 284 and Section 12 1 5 on page 285 12 1 1 The SCHRODINGER Environment Variable Before running Jaguar on any particular machine you must set the environment variable SCHRODINGER to point to the installation directory on that machine This is the directory Jaguar 5 5 User Manual 281 Chapter 12 Troubleshooting containing Jaguar version 5 0 which is in a subdirectory called jaguar vxxxxx where xxxxx 1s the five digit version number To check whether the SCHRODINGER environment variable is set enter the command echo SCHRODINGER 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 tcsh setenv SCHRODINGER installation directory sh bash ksh export SCHRODINGER installation directory You should also set the SCHRODINGER environment variable in your shell sta
200. antum 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 fragment based methods Optimal use of the methodology in this fashion is accomplished by performing solution phase conformational searches with the MacroModel molecular modeling code Third the method can handle multiple protona tion 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 5 5 User Manual 299 Chapter 14 The pKa Prediction Module 14 2 Theory of pK Calculation 14 2 1 Abinitio Quantum Chemical Calculation of pK Values The calculation of the pK of a molecule in aqueous solution can be represented as a ther modynamic cycle A BH gt Bg Ho BH gt B H aq aq aq The strategy in our pK
201. any other atom the Pipek Mezey orbital is considered to be localized on that single atom and that Pipek Mezey orbital will be included in any LMP2 calcula tion for which that atom is specified in any requested LMP2 atom pairs 4 2 2 Setting up an LMP2 Calculation Jaguar will not perform an LMP2 calculation unless you make a selection under Corre lated Pairs to indicate which atoms should be treated at the LMP2 level To perform an LMP calculation that includes all atoms select LMP2 all pairs You can perform a local local MP2 calculation by selecting a subset of atoms to be treated with LMP2 while the remaining atoms are treated at the HF level Jaguar includes a setting to treat 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 solva tion calculations using LMP2 To request such a calculation select LMP2 hetero pairs 6 To specify atom pairs yourself select LMP2 user input pairs and choose the LMP2 pairs using the three sliders in the LMP2 window To specify the first LMP2 pair leave the 25 Keyword mp2 3 in gen section of input file 26 Keywords iheter 1 and mp2 3 in gen section of input file 27 If you were editing an input file directly instead of using the GUI you would need to set LMP2 pairs in the Imp2 section of the i
202. ar two options are available for frequency scaling the Pulay et al Modified Scaled Quantum Mechanical Force Fields SQM method 60 for B3LYP calcu lations using the 6 31G basis set and standard frequency scaling in which all frequen cies are simply multiplied 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 mole cules containing C H N O and Cl using the 6 31G basis set Jaguar permits only the SOM scaling method to be used for B3LYP 6 31G frequency jobs You can turn on SOM scaling for these jobs from the Frequencies window by setting the option menu labeled Pulay SQM scaling to B3LYP 6 31G factors The method is off by default 52 Keyword ifreq 1 in gen section of input file 53 Keyword massav 0 in gen section of input file 54 Keyword massav 1 in gen section of input file 55 Keyword isqm 1 in gen section of input file 56 Keyword isqm 0 in gen section of input file 66 Jaguar 5 5 User Manual Chapter 4 Options Alternatively for any type of frequency job you can multiply all frequencies by the same scale factor by changing the value in the text box marked Frequency scaling Table 4 2 lists recommended scale factors for various methods and basis sets The factors in the
203. ar geom etry output from the pre program This section describes the changes in output for various calculation settings described in Chapter 4 Generally only the format changes that result from these settings are discussed below Naturally these settings will often change the data listed For information on the settings themselves see Chapter 4 Options that have no significant impact on the output format are not discussed in this section 6 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 calculations includes the breakdown of the two electron energy into Coulomb and exchange correlation terms For DFT calculations virtual orbitals are obtained by diago nalizing Ho d 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 eigen values The scf output from post SCF 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 treatment does not change the wavefunction no orbital output is reported from this step The output from the program pre for non default options contains the detailed description of customized functio
204. arge and Multiplicity State You can set the charge and the spin multiplicity of the molecule in the Molecular State window which you open by clicking the State button in the Geometry section of the Jaguar panel The default molecular charge is 0 and the default spin multiplicity is singlet if the molecule has an even number of electrons and doublet if it has an odd number of electrons You can change the spin multiplicity to anything up to octet by choosing a value from the Spin Multiplicity list and to a higher value by choosing other and entering a value in the multip 2S 1 text box The spin multiplicity is always displayed in this text 2 Keyword molchg in gen section of input file 3 Keyword multip in gen section of input file Jaguar 5 5 User Manual 33 Chapter 3 Running Jaguar From Maestro Molecular State Molecular Charge 1 Spin Multiplicity singlet mid p 23etY i OK Cancel Help Figure 3 3 The Molecular State window box If the molecular charge and spin multiplicity settings you make do not agree for your molecular input for instance if your molecule has an odd number of electrons and you set the spin multiplicity to singlet Jaguar warns you to reset one or the other 3 4 Reading Files If you already have files containing geometries either with or without information on the type of calculation to perform you can read them using the Read File window which you open by clicking the Read
205. arization functions on all atoms except H and He 64 Keyword basis in gen section of input file 70 Jaguar 5 5 User Manual Chapter 4 Options 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 molecules that include atoms with negative charges Table 4 3 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 polarization functions by definition Note that in versions 2 3 and earlier of Jaguar the cc pV TZ basis set did not include f functions and therefore corresponds to the current cc pVTZ f Table 4 3 also indicates the method used for the calculation the fast pseudospectral method or the slower analytic method in which four center two electron integrals are computed explicitly as in conventional ab initio programs 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
206. arply 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 remaining functions are classified as long range functions which are all considered to be in one single group 13 Since Q does not depend on the wavefunction itself it can be fully computed before the SCF procedure However since the Q for each grid type contains Ny x Noria elements where N is the number of basis functions and N iq the number of grid points which is generally larger than N41 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 1 1 ie T Tig where and are basis functions and the index g represents a grid point These inte grals are calculated for all combinations of basis functions a
207. ase 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 environ ment 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 that MP HOSTFILE to the file that contains the host list If MP_HOSTFILE is not set then the hostfile is assumed to be called host 1ist and to reside in the current directory see the poe man 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 processor in that node For example if you have a workstation 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 for more information Ensure that the schrodinger hosts file is properly configured for your cluster See Section 11 1 4 on page 266 for more information on this file Fi
208. asis 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 5D or 6D sets the default number of functions for d shells when using that basis set as described in Section 4 8 on page 70 Backup basis set names which are each preceded by the word BACKUP may 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 func tions 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 s 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 being described S P or D for instance If t
209. asis 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 func tions 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 4 9 6 on page 78 or the information on the input file gen section keyword nops in Section 9 5 15 on page 193 To use the file in a Jaguar calculation you must add a line in the form BASISFILE lt basis file path and name gt 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 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 2080 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 SSCHRODINGER utilities makejbasis input filename output filename Jaguar 5 5 User Manual 241 Chapter 10 Other Jaguar Files 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 Per
210. at is well described by the Hessian by 9 Keyword inhess 1 in gen section of input file 10 Keyword inhess 0 in gen section of input file 11 Keyword inhess 1 in gen section of input file 12 Keyword inhess 4 in gen section of input file 13 Keyword itradj 0 in gen section of input file 14 Keyword itradj 1 in gen section of input file Jaguar 5 5 User Manual 85 Chapter 5 Optimizations and Scans increasing the trust radius when the Hessian is correctly predicting energy changes and decreasing it when the predictions are inaccurate At the beginning of a job the trust radius starts at the value in the box marked Trust radius For gas phase optimizations to minimum energy structures the default initial trust radius is 0 3 atomic units for solvation calculations or transition state optimizations the default initial trust radius is 0 1 atomic units 5 2 Constraining Coordinates To constrain certain coordinates to stay frozen unchanged or equal to each other during an optimization you can use the Geometry Optimization window settings or the Edit window The first subsection of this section describes how to freeze an entire class of coor dinates during an optimization The other subsections describe ways to constrain indi vidual coordinates by editing the geometry input 5 2 Freezing All Bond Lengths Bond Angles or Torsional Angles You can freeze all bond lengths all bond angles and or all torsiona
211. ate key words 169 Molecular State window 33 34 molecular structure see geometry input or ge ometry optimization Moaller Plesset second order perturbation theory see MP2 Monitor panel see 25 40 mouse functions eeesssessseeeeereeen 14 MP HOSTFILE environment variable 297 MP RMPOOL environment variable 297 MP2 Mgller Plesset second order perturbation theory cene 54 56 156 158 keywords for cescssceeceeeeeeeeeeeeeeeees 172 output from eene 106 107 MPI flags setting eee 298 MPI PASSPORT environment Variable a fati te etian 293 295 MPI USEPASSPORT environment variable ju e tto 293 295 MACH utlity 5 5 293 205 MOM basis set file bas keyword for 207 Mulliken population analysis 64 for basis functions we 64 Key Word for ett 190 output from 120 121 output of multipole moments from 121 338 recalculating multipole moments POMS ne hee aescceve 62 64 Mulliken spin populations 64 multiple Jaguar jobs running from Maestro sese 40 44 with jaguar batch 275 280 multiplicity keyword for entre 169 Setting foi iieiaei rtis 33 34 multipole moments calculating niis 62 141 constraining electrostatic potential fitting to reproduce 61 117 1
212. ated 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 atomic 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 calcula tion 2 Perform Pipek Mezey localization on valence orbitals for LMP2 calculation maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on valence orbitals for LMP2 calculation maximizing Mulliken basis function populations 9 5 7 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 wavefunction using a particular set of functionals you can use the jdft keyword Most DFT options described here are also available from the GUI as described in Section 4 1 on page 49 For information on setting the keywords associated with grids for DFT calculations see Section 9 5 23 on page 210 The dftname keyword can be given as a standard functional name as listed in Table 9 8 or it can be constructed from a set of functional name strings for exchange and correlation function
213. ation for valence electrons only iheter 0 Treat all atoms with LMP2 if 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 elements 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 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 7 atoms over all atoms in the aromatic ring 172 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 7 Keyword Settings for Local MP2 Calculations Cont d Keyword Value Description idelocv 0 Do not delocalize any pairs listed in Imp2 section default for all calculations except those with iqst gt 0 and or ireson 0 1 Treat all LMP2 pairs but delocalize any pairs in Imp2 section as indicated there or default for QST guided transition state searches delocalize any pairs on atoms with breaking or form ing 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 indic
214. ation 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 itera tion or density difference matrix if Fock matrix updating was done ip121 All J and K matrices in atomic orbital space ip122 Fock matrix in atomic 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 Seetext in this subsection for information on ip152 9 5 22 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 in which the orbital output appears 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 Hq 25 2J K where f is the 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
215. atives of energy as numerical derivatives of the analytical gradient freq Calculates vibrational frequencies and related properties ira irb Calculate dipole derivative terms needed for calculation of IR intensities 232 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 46 Individual Programs Included in Jaguar Cont d Program Description geopt Performs geometry optimization pbf Solves Poisson Boltzmann equations for solvation calculation solv Performs solvation calculation using results from Jaguar Poisson Boltzmann solver sole Checks solvation energy convergence dsolv Computes solvation related gradient terms for solvated geometry optimiza tions post Processes files output etc at end of run timex Checks CPU time for entire run machid Utility program returns machine information note not used in Jaguar calcu lations 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 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 s
216. 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 Hybridization labels must start with five spaces followed by one of the following char acter strings s hybridization p hybridization d hybridization sp hybridization sp2 hybridization sp3 hybridization sp3d hybridization sp3d2 hybridization 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 indicates 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 Jaguar 5 5 User Manual 257 Chapter 10 Other Jaguar Files HYBRIDIZATION TYPE 01 INFORMATION 1 HYDROGEN Group 1
217. atoms in your molecule If you select an italicized basis set name the calculation will run all analytically without using the pseudospectral method All of these settings are explained further below 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 You can perform counterpoise calculations with Jaguar adding counterpoise atoms that have the usual basis functions for their elements but include no nuclei or electrons However counterpoise atoms should be entered through the Edit window rather than the Basis Set window See Section 3 2 on page 26 if you want to use counterpoise atoms For any basis set with the option choosing places polarization functions on all atoms unless the basis set uses effective core potentials in which case polarization functions are placed only on atoms not described with effective core potentials For STO 3G and 3 21G basis sets choosing places polarization functions on all atoms found in the third row Na Ar or higher rows for STO 3G of the periodic table For effective core potential basis sets CSDZ and those whose names begin with LA choosing places polarization functions on all atoms not described by effective core potentials except H and He For all other basis sets places pol
218. ave the desired molecular symmetry or it might be far from the minimum or transition state Jaguar has options to clean up the geometry for calculations in both of these cases The options are available from the Geometry Cleanup window which you open by clicking Cleanup in the Jaguar panel The changes made in this window are not applied until you click OK To check the effect on the geometry you must close the window and open the Edit Geometry or Edit Input window If you want to be able to restore the previous geometry after inspecting the new geometry save the geometry using the Save dialog box before opening the Geometry Cleanup window 3 5 1 Quick Geometry Optimization When you click Clean up geometry in the Geometry Cleanup window Jaguar 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 the label on the Clean up geometry button changes to Halt cleanup Click this button at any time to stop the minimization After the cleanup is finished Jaguar reanalyzes the symmetry of the molecule and displays the point group of the minimized structure If you are satisfied with the results of the cleanup p
219. be accurate enough to be a reasonable representation of the final transition vector To refine an initial Hessian first choose low frequency modes from the Hessian refinement option menu in the Transition state search window which should open when you select transition state search in the Optimization window s first option menu Next you must specify the number of low frequency Hessian eigenvectors to be used in the refinement or you must specify one or more input coordinates for refinement You can also use both low frequency modes and particular coordinates for a refinement Section 5 3 7 explains how to select input coordinates for refinement If you want to specify a certain number of low frequency eigenvectors edit the number in the box marked of low freq modes By default no eigenvectors are used that is no refine ment 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 accurate information about the most important modes to be included in the Hessian 33 Keyword irefhup 3 in gen section of input file 92 Jaguar 5 5 User Manual Chapter 5 Optimizations and Scans 5 3 7 Specifying Coordinates for Hessian Refinement If you are optimizing a molecular structure to obtain a minimum energy structure or a
220. ber before the dash A zero indicates that the contracted function 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 symmetriza tion of the Fock matrix components by the side choosing method described in reference 13 These range values are only used in pseudospectral calculations so if your basis set 238 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files will be used for non pseudospectral calculations use a 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 de ault gridand 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 coefficient 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
221. bitals 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 nega tive 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 will be known 216 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File The sample gvb section which follows sets a sigma bond pair with RCI on between atom 1 and atom 2 and two lone pairs on atom 1 amp gvb 1 I1 2 1 10111 10211 amp 9 7 The Imp2 Section The Imp2 section whose GUI equivalent is described in Section 4 2 on page 54 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 of labels which specify the two atoms in the pair Pairs can be listed in any order The sample Imp2 section which follows instructs Jaguar to treat the atoms listed sixth ninth and tenth in the zmat section at the LMP2 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 o
222. 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 14 3 Predicting pKa Values in Complex Systems The algorithm described in Section 14 2 on page 300 can be straightforwardly applied in the simplest cases which are characterized as follows 1 There is only one relevant ionizable group 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 accom plished 14 3 1 Conformational Flexibility First consider the case in which assumption 1 above holds but the protonated and deprotonated states can each exist in multiple conformations which might be energeti cally competitive 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 the user must run multiple jobs and manually assemble the data into a final result 1 Perform calculations on one protonated and one deprotonated conformation which are assumed to dominate the phase s
223. 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 For medium and large molecules the additional overhead the pseudospectral method requires to compute the information needed for the transformation between physical and spectral space is vastly outweighed by the advantages of evaluating the integrals in phys ical space The matrix needed for the transformation from physical to spectral space 7 can be assembled before the SCF iterations by calculating 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 func tions and dealiasing functions which are chosen in order to span the function space repre sented by the 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 Jaguar 5 5 User Manual 147 Chapter 8 Theory In practice not all possible Qi elements are calculated for each basis function i and each grid point g because most basis functions drop off sh
224. c units where V is the nuclear potential and J is the Coulomb poten tial Therefore for a given exchange correlation functional it is possible to solve itera tively for Kohn Sham orbitals w r and the resulting density p to yield a final DFT energy A more detailed description of density functional theory can be found in references 112 and 113 160 Jaguar 5 5 User Manual Chapter 9 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 that present keyword values and definitions the default value is set in bold italic 9 1 General Description of the Input File The input file often begins with an optional line indicating the version number of Jaguar such as v50012 The other parts of the input file are either single lines composed of options in capital letters foll
225. 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 can then be used to generate high quality initial guesses for these systems See Section 7 1 1 on page 139 for more information on using atomic sections in this manner 9 8 1 General Format of the atomic Section After the amp atomic or atomic line the atomic 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 also the column heading row Subsequent rows list the corresponding values for the keywords for each relevant atom For instance in the following atomic section amp atomic atom mass vdw2 H1 2 00 11 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 a solvation calculation and the lines for the atoms H1 and H2 specify that these atoms have a nuclear mass of 2 00 amu deuterium and van der Waals radii of 1 2 A for solvation purposes
226. can be requested for each other keyword determining the orbitals printed The choice of keywords which are listed in Table 9 34 determines 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 6 7 on page 133 Table 9 35 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 occupied 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 208 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 34 Keywords to Specify When to Output Orbitals Keyword Prints Orbitals ip100 For initial guess from before SCF generally redundant with ip105 ip101 In canonical orbital space each SCF iteration ip102 At end of job ip103 In atomic orbital space each SCF iteration ip104 In atomic orbital space after SCF ip105 For HF initial guess ip106 For GVB initial guess ip107 After Boys or Pipek localization Table 9 35 Dependence of the Format and Type of Orbital Output on the Value of ipx Value of ipx 2 n 34 n 4 n 54 n 6 n Format f5 2 f10 5 f19 15 f8 5
227. ce Sequence viewer displays the sequences for proteins currently displayed in the Workspace Command input area provides a way to execute Maestro commands 2 3 Maestro Projects The project is a central concept in Maestro A project is a collection of chemical structures entries and their associated data These structures and their data are represented in the Project Table which displays an ordered list of entries and any associated data You can open the Project Table panel by choosing Show Table from the Project menu There is always a project open in Maestro If you do not specify a project when you start Maestro a scratch project is created You can work in a scratch project without saving it but you must save it in order to use it in future sessions Entries are represented by rows in the Project Table Each row contains the row number the title the entry s Workspace inclusion state the In column a button to open the Surfaces panel if there are surfaces associated with the entry the entry name and any properties associated with the entry If there are no surfaces associated with any entry the Surf column of the Project Table is empty Jaguar 5 5 User Manual 7 Chapter 2 The Maestro Graphical User Interface Project Table table Table Select Selection Columns Total Entries 23 Subset Entries 23 Selected Entries 2 Tithe in SurflEntry Name Minimization fe 01 820 1ig 12 im
228. ce 78 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 wavefunction has been requested at end of job Print the orbitals at the end of the job 25 26 27 28 29 30 Keyword ip105 in gen section of input file Keyword ip106 in gen section of input file Keyword ip101 in gen section of input file Keyword ip103 in gen section of input file Keyword ip104 in gen section of input file Keyword ip107 in gen section of input file Jaguar 5 5 User Manual 133 Chapter 6 Output What By default no orbitals are printed in the output file so the selection none appears in the What option menu If you select occupied orbitals all occupied orbitals including GVB 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 information on the keyword ipvirt in Section 9 5 22 on page 208 The virtual orbitals are obtained by diagonalizing 7 by f 2J K where fis the fractional occupation of each orbital 1 for a closed shell Selection of GVB orbitals nonorthog prints only the GVB non orthogonal orbitals How The choices available for how to print the selected orbitals are large elements as f5 2 labels in list all element
229. ch 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 de ault grid file for Jaguar version 5 5 begins as follows gridv0220 5 24 BASIS 6 31G Jaguar 5 5 User Manual 249 Chapter 10 Other Jaguar Files coarse grid 1 16 0 23021 0 71955 1 74518 2 82595 3 94135 6 40743 13 7 7 3 1 2 20699 0 45860 0 97184 1 61794 2 40119 3 26487 5 20964 3 q 9 p3 d pe 3T 0 59584 1 69094 3 39571 5 30494 7 49262 11 30338 16 61803 4 3 7 9 731 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 each atom corresponding to the coarse medium fine ultrafine and gradient grids All coarse grids for 6 31G with or without the polarization functions indi cated by the will set the boundary plane between atoms described earlier at the
230. chr dinger contact information SCHRODINGER directory SCHRODINGER environment variable 5 282 SCHRODINGER MPI FLAGS environment Variable ite eiecti 295 298 SCHRODINGER NODEFILE environment Variable tee a cedet 293 295 SCHRODINGER POE FLAGS environment Variable iioniantiana raria 298 SCHRODINGER TMPDIR environment vari AD Ess 266 schrodinger hosts file 38 39 263 266 269 286 287 scratch entry project table 9 Scratch project eee eiecti p SCRF method for solvation calculations 58 59 112 search method transition state 89 searching along paths and eigenvectors 91 second derivative of energy keywords for 182 184 192 secure servers MPICH 293 selecting atoms eere 10 self consistent reaction field method for solva tion calculations sess 58 50 semaphores freeing shared memory building MPICH with 291 342 shells information in output 103 Simons method for trust radius adjustment key wOrd Tor aet tete 183 singlet open shell keyword for 199 Soleprogtam 3e netten 233 output from 2 nee 115 SOLV Progra senises esas 233 output from sese 113 SOLyatlOnL 2 iens ii et tintas 58 60 energy output seseina iesist 115 keywords for
231. ck failed 1 then all available semaphore sets are taken on at least one of the nodes This error can only occur when using shared memory If you have dual CPU machines and you compiled the Linux kernel for SMP this error can occur if you did not build MPICH with the with comm shared option It can also occur if other users are running jobs that use shared memory or if many previous Jaguar jobs failed in such a way that the semaphores could not be freed To check for semaphores that are not freed enter the command SSCHRODINGER utilities mpich sems Jaguar 5 5 User Manual 295 Chapter 13 Parallel Jaguar If the output indicates that you are still using semaphores for jobs that are no longer running enter the command SSCHRODINGER utilities mpich rmsems to free them You should also check for running processes that are associated with failed Jaguar jobs with the command SSCHRODINGER jaguar jobs You can kill all processes associated with a job whose status is running by entering the command SCHRODINGER jaguar kill jobcontrol id The processes associated with any jobs listed as stranded must be killed manually If the jobname out file contains an error message like the following pl 28583 19 611297 xx shmalloc returning NULL requested 3251504 bytes pl 28583 19 611409 p4 shmalloc returning NULL request 3251504 bytes You can increase the amount of memory by setting the environment variable PA GLOBMEMSIZE in byte
232. column headed of d fns indicates whether d shells include the five functions d dyz dyz dy2_ 2 and d52 2 2 all with the same angular momentum l 2 or whether d shells include the six second order Cartesian d functions d 2 d yt d2 d xy d and d This choice also affects the dimension of the Fock matrix for diagonaliza tion To override this selection set the keyword numd in the gen section of the input file as described in Section 9 5 14 on page 193 The orbital coefficients are always printed out in terms of the six Cartesian functions The full references describing the basis sets are in the References list at the back of this manual Table 4 3 Available Basis Sets That Do Not Include Effective Core Potentials Atoms of Basis Set Included Options Method d fns Refs STO 3G H Xe Na Xe analytic 5 62 66 3 21G H Xe Na Ar H Ar pseudospectral 6 67 69 Li Ar analytic with or H Ar K Xe analytic 4 21G H Ne TT analytic 6 70 6 21G H Ar ORE analytic 6 67 69 4 31G H Ne Tem analytic 6 71 76 6 31G H Zn RRS p o RE H Ar pseudospectral K Zn 6 72 78 for H Ar analytic Jaguar 5 5 User Manual 71 Chapter 4 Options Table 4 3 Available Basis Sets That Do Not Include Effective Core Potentials Continued Atoms of Basis Set Included Options Method d fns Refs 6 311G H Ar o H Li C F Na Si Cl pseu 5 79 82 dospectral others analytic 6 311G 3df H Ar analytic 5 79
233. cting classes of entries on the Select menu and in the Select panel You can open the Select panel from the Select menu You can use entries as input for all of the computational programs Glide Impact Jaguar Liaison MacroModel Prime QikProp and QSite You can select entries as input for the ePlayer which displays the selected structures in sequence You can also duplicate combine rename and sort entries create properties import structures as entries and export structures and properties from entries in various formats 8 Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface When you build molecules in the Workspace they constitute the scratch entry until you save the structures as project entries The scratch entry is not saved with the project unless you explicitly incorporate it into the project However you can use a scratch entry as input for some computations 2 4 Building a Structure After you start Maestro the first task is usually to create or import a structure You can open existing Maestro projects or import structures from other sources to obtain a struc ture To build a structure you use the Build panel which you can open by clicking the hammer icon in the toolbar or by choosing Build from the Edit menu Build build Delete O Pick Atom All Select J W Also delete terminal atoms Atoms Connect amp Hydrogen Display amp Options Bonds Fuse Treatment Un
234. culation is to be performed the calculation host are the same The best method to test whether this problem is occurring is to issue individual rsh commands at a local host command line prompt such as rsh calculation host who where you substitute the name of the host where you want to perform the calculation for calculation host If both the local and calculation 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 given host in its etc hosts equiv file It may be necessary to include the name of the local host in its own etc hosts equiv file if the calculation is to be done on the local 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 Temp directory bar in the Run window 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 calcula tion hosts are not local to each other you must include the local machine in a rhosts file in your home directory on the calculation host and vice
235. culations irder 0 Do not compute dipole derivatives or IR intensities for vibra tional frequencies 1 Compute derivatives of dipole moment and IR intensities for vibrational frequencies see text for details 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 tempera tures for thermochemical calculations in K default is 10 0 ntemp gt 0 Number of temperatures at which thermochemical properties are computed default is 1 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 9 16 on page 231 to tell Jaguar the appropriate sequence of executables to run in order to calculate dipole derivatives only The path section to use is 192 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File amp path pre onee hfig probe grid rwr scf ira rwr irb amp You must also set irder 1 and isymm 0 and igeopt 1 The igeopt setting is necessary to force tight accuracy in the SCF but no optimization 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
236. d along the positive z axis For example N1 C2 N1 1 4589 places the carbon atom C2 at 0 0 0 0 1 4589 in Cartesian coordinates Distances between atoms must be positive 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 14 5203 N1 115 32 the final line states that atoms C3 and C2 are separated by 1 5203 A and that the C3 C2 N1 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 N1 115 32 O4 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 colinear or very nearly colinear O4 s position would be poorly defined You should avoid defining
237. d change entries during the animation 57 Keyword scalfr in gen section of input file Jaguar 5 5 User Manual 67 Chapter 4 Options 2034 079 623 170153 Animate Amplitude 1 000000 Slower Faster Speed aE OK Figure 4 7 The Vibration panel If you did not run the frequency job from the Jaguar panel the vibrational data is not incorporated because the molecule is not a project table entry To view the animation 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 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 Click Edit Input to edit the restart file 3 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 4 Run the job 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 pan
238. d for esee 195 COTY nce iti R 149 analytic frequencies 65 66 analytic gradient of energy 83 84 convergence criteria sess 84 in output file eese 111 input keywords for 180 184 angles see bond angles atom labels bond lengths and angles in output 125 canonical orbital space 135 200 format e 28 GVB pairs sce in orbital output sss 209 IM O tput aie ete tede 102 in zmat section sse 164 in Z matrix input sese 20 LMP2 paits oen eeteeleine 56 Mulliken population output 120 orbitals in output sese 134 atom numbers for GVB pais aa esce 24 for LMP pairs tnter 56 atom selection inann naa 10 Atom Selection dialog box 11 atomic charges from ESP fit oreet 60 Mu lliken titre 64 atomic charges formal 220 atomic charges see electrostatic potential fiting Mulliken population analysis molecular charge Jaguar 5 5 User Manual atomic masses for frequency calculations 66 input keyword for 169 setting in atomic section 218 220 atomic orbital space output in 132 133 atomic properties setting in atomic SECHON God
239. d for output of 208 energy convergence criterion at keyword Tor etn tae 193 energy difference as geometry convergence criterion 84 111 keyword for geometry convergence CHILCTION iiie nete tret era raro 184 energy output final GVB components 107 final SCF components 105 SCF components for each iteration 131 208 solvation esses 113 116 total SCF for each iteration 105 137 Jaguar 5 5 User Manual two electron contributions when OCBSE selected 123 enthalpy calculations see thermochemical properties entropy calculations see thermochemical properties environment variables DISPLAY eet 5 283 JAGUAR SCRATCH 266 JAGUAR SCREPTS ueteri 4 MP HOS PEEBEE ions cs eieeseeeeesec ees 297 MP RMPOOL eren 297 MPI PASSPORT iet 293 295 MPI USEPASSPORT 293 295 P4 GLOBMEMSIZE ee 296 BATH oen A ets 282 291 SCHRODEINGER ite eise ette enean 5 282 SCHRODINGER MPI FLAGS 295 298 SCHRODINGER MPISTART 294 SCHRODINGER NODEFILE 293 295 SCHRODINGER POE FLAGS 298 SCHRODINGER TMPDIR 266 ESP see electrostatic potential exchange corrections in pseudospectral calculations tente 254 exchange operator K contributions to energy 131 keyword for per iteration output 208 keywords for calculation of
240. d 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 9 5 4 Symmetry Related Keywords By default for most calculations Jaguar takes advantage molecular symmetry to reduce computing time as described in Section 3 5 2 on page 37 Several integer valued keywords shown in Table 9 5 describe how the program uses symmetry Jaguar 5 5 User Manual 169 Chapter 9 The Jaguar Input File Table 9 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 repre sentation default for HF and DFT closed shell jobs 1 Don t allow number of electrons in each irreducible representa tion to change default for non HF non DFT and open shell cal culations idoabe 0 Allow non Abelian point group symmetry assignment 1 Allow only Abelian point group symmetry assignment 9 5 5 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
241. ded The file always contains a molecular geometry in Cartesian coordinates and ngstr ms instruc tions for how to input geometries are available in Section 3 2 on page 26 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 Molecular State window You can also set the name of the basis set you want to provide in the 992 file for example STO 3G using the Basis Set window The default basis set choice is 6 31G To actually generate the 992 file you need to run the Jaguar job you have just specified See Section 3 6 on page 38 for information on running jobs 7 3 1 1 Making Input Files for GVB Calculations To set up the 992 file for a GVB calculation you should use the default setting Compute from HF initial guess from the GVB initial guess option menu which is in the Methods window You should specify the GVB pairs in the GVB window as well See Section 4 3 on page 56 for information on setting up GVB calculations If you have selected a GVB calculation symmetry is automatically turned off and the g92 file also specifies nosymm You might want to delete this setting from the 992 file after it is produced The 992 file also contains a Jaguar generated initial guess if you have selected a GVB calculation and notes that this trial wavefunction is to be used as an initial guess for the GAUSS
242. default for transition state optimizations 1 Adjust trust radius using Simons cubic potential model 125 not recommended with Jaguar itrcut 0 Apply trust radius by truncating Newton Raphson step s 1 Apply trust radius by level shifting of Hessian to reduce resultant step size The real valued keywords that control optimizations are listed in Table 9 18 and Table 9 19 Note that all keyword values must be greater than or equal to zero The keywords shown in Table 9 19 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 real valued keywords listed in Table 9 19 have units of hartrees bohr gconv5 and gconv6 have units of bohr and gconv7 has units of hartrees Note also that 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 Jaguar 5 5 User Manual 183 Chapter 9 The Jaguar Input File Table 9 18 Real valued Optimization Keywords Except for Convergence Criteria Keyword Description pertnd qstinit Displacement in atomic units used for Hessian refinement or calculations of numeric
243. der in which the corre sponding data is printed The options are listed in Table 6 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 intermediate 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 struc ture Each of these types of results tables are described below Data values for each output file are printed with results for each job on a separate line Jaguar 5 5 User Manual 97 Chapter 6 Output Table 6 1 Options for the jaguar results Command Option Meaning Job and Molecular Information Options jobname longjobname stoich weight basis nbasis nelectron npair nsigma npi natom symmetry nsymm charge multip s2 sz2 method job name job name with wider output stoichiometry molecular weight basis set number of basis functions number of electrons number of electron pairs number of sigma electron pairs number of pi electron pairs number of atoms molecular symmetry symmetry number molecular charge spin multiplicity spin lt S 2 gt s
244. ding Cutoff sets are explained in the cutoff file description in Section 10 5 on page 252 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 9 5 23 on page 210 and Section 10 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 calcu lations 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 The nuclear repulsion one electron two electron and electronic contributions are all listed followed by the total Each of these energies is labeled with a letter for example A for the nuclear repulsion and information to the right of some of
245. display Acid C 0 Acid 0 C Alkene Alkyne Amide C gt N Ami de N C Amine Ammonium Carbonyl Cyclobutyl Cyclohexyl Cyclopentadieny Cyclopentyl Cyclopropyl Hydrogen Hydroxide Hydroxyl Methyl Grow Direction forward Joining Geometry anti a Figure 2 3 The Build panel Jaguar 5 5 User Manual 9 Chapter 2 The Maestro Graphical User Interface The Build panel allows you to create structures by placing atoms or fragments in the Work space and connecting them into a larger structure to adjust atom positions and bond orders and to change atom properties The Fragments folder offers a variety of molecular fragments from which to build a structure To place a fragment in the Workspace select the fragment and click in the Workspace where you want the fragment to be placed You can place several fragments in the Workspace and connect them using the Connect amp Fuse tab you can attach a fragment to a structure by selecting it and clicking on an atom in the Workspace or you can place a fragment and grow another fragment onto it by defining a grow bond and then selecting a fragment The new fragment replaces the atom at the head of the arrow on the grow bond and all atoms attached to it To draw a structure freehand use the Draw feature of the Atoms amp Bonds tab Once you have a structure you can adjust the bond lengths bond angles and dihedral angles using the Adjust tab In the Atoms amp Bonds
246. e porq ONU Jaguar 5 5 User Manual 51 Chapter 4 Options BP86 VWN5 Exchange Slater local functional 29 Becke 1988 nonlocal gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Per dew 1986 gradient correction functional 35 PWP91P Exchange Slater local functional 29 Perdew Wang 1991 gradient cor rection functional 31 correlation Perdew Wang 1991 GGA II local and nonlocal functionals 31 HCTH407 Hamprecht Cohen Tozer Handy functional including local and nonlo cal exchange and correlation reparametrized with a training set of 407 molecules by Boese and Handy 40 PBEP Perdew Burke Ernzerhof local and nonlocal exchange and correlation func tional 41 Hybrid functionals B3LYP 6 Exchange exact HF Slater local functional 29 Becke 1988 nonlocal gra dient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Lee Yang Parr local and nonlocal functional 33 See refs 27 and 28 B3PwWeo1 Exchange exact HF Slater local functional 29 Becke 1988 nonlocal gradient correction 32 correlation Perdew Wang 1991 local and GGA II nonlocal functional 31 B3P86 Exchange exact HF Slater local exchange functional 29 Becke 1988 nonlocal gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Perdew 1986 nonlocal gradient correction 35 BHandH 50 exact HF exchange 50 Slater local exchange functional 29
247. e 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 s 6 13E 05 5 13E 05 The last section of Table 6 1 lists the options that let you specify when to report interme diate and final results from jobs The a11 option which lets you track the progress of a geometry or transition 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 Jaguar 5 5 User Manual 101 Chapter 6 Output 6 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 coordi nates forces or charges for individual atoms are listed in the per atom information options section of Table 6 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 i
248. e mm2in MM2 Input file mm2out MN2 Output file mm3 MM3 file mmads MMADS file 202 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 30 Output Format Keywords and File Types for Babel File Format Conversions Cont d Format Keyword File Type mdi MDL Molfile file miv MolInventor file mopcrt Mopac Cartesian file mopint Mopac Internal file csr MSI Quanta CSR file pemod PC Model file pdb PDB file psz PS GVB Z Matrix file psc PS GVB Cartesian file report Report file smiles SMILES file spar Spartan file mol Sybyl Mol file mol2 Sybyl Mol file maccs MDL Maccs file torlist Torsion List file tinker Tinker XYZ file unixyz UniChem XYZ file XYZ XYZ file xed XED file 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 9 30 You can set babel more than once using separate babel outext assignments if you want to generate several files To generate output files at the end of each iteration in a minimum energy structure or tran sition state 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 Jaguar 5 5 User Manual 203 Chapter 9 The Jaguar Input File As files are generated with Babel during Jaguar runs
249. e you can use the Atom Selection dialog box To open this dialog box click Select You can select an atom grouping from any of the tabs in the dialog box Atom Residue Molecule Chain Entry Substructure Notation or Set You can then combine this grouping with another grouping using the buttons on the right the Add button Boolean OR includes the current selection with the existing selection the Remove button Boolean AND NOT excludes atoms in the current selection from the existing selection and the Intersect button Boolean AND includes only those atoms that 10 Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface Atom Selection Delete atom Residu Molecule cnain entry meu set Atom Number Atom Number In Entry Atom Number In Molecule Atom Number In Entry Atom Name Element Ei PDB Type MacroModel Type Examples Hydrogens 12 or 3 5 20 34 Formal Charge Partial Charge Number of attachments Range In Workspace Update Markers Display State 1 12 Backbone side Chain Atoms Matching o ASL W Show Markers LAU unde Matching 0 atoms OY Cancel Figure 2 4 The Atom Selection dialog box are in both the current selection and the existing selection The existing selection is expressed in ASL language in the ASL text box and is shown with light blue markers in the Workspace The current selection is shown with purple markers When you are
250. e 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 launch the MPICH secure server enter the command SSCHRODINGER utilities mpich start p port The port number port should be a four digit number greater than 1023 If p port is not specified the value of MPI PASSPORT is used for the port number If MPT PASSPORT is not set the default value of 1234 is used Although each user may launch the secure server and select a port number for private use we recommend that the system administrator launch the server as root so that all users can use the same port number The port number should be different from the default 1234 to avoid conflicts with other uses of the secure server ports The mpich start command launches the secure servers on all of the hosts listed in the machines LINUX file To use the secure servers the following environment variables must be set csh tcsh setenv MPI USEPASSPORT yes setenv MPI PASSPORT port sh ksh bash export MPI USEPASSPORT yes export MPI PASSPORT port The port number assigned to MPT PASSPORT must match the port number used to launch the secure server These environment var
251. e 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 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 Jaguar 5 5 User Manual 113 Chapter 6 Output start of program scf ae ke dE X dd t p 4x oE RMS maximum e d i u i energy density DIIS r te S tod total energy change change error etot 1 NN 2 U 76 03
252. e canonical MP2 energy correction The pseudospectral implementa tion of LMP2 is described in Section 8 4 on page 156 4 2 1 Summary of the LMP2 Method in Jaguar For closed shell systems you can perform LMP2 geometry optimizations charge fitting solvation calculations and most other options available with HF wavefunctions Local MP2 geometry optimizations employ analytic gradients For calculations of LMP2 dipole moments Jaguar computes a coupled perturbed Hartree Fock CPHF term 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 4 6 1 on page 60 and Section 4 6 2 on page 62 Jaguar s implementation of the local MP2 method requires basis sets that allow the pseu dospectral method to be used This basis set information can be found in Section 4 8 on page 70 and in several of the periodic tables of information by element beginning on page 222 A warning is displayed if you choose a non pseudospectral calculation Local MP2 Correlated Pairs LMP 2 user input pairs Atom Pair Atom 1 Atom 2 Figure 4 2 The Local MP2 window 54 Jaguar 5 5 User Manual Chapter 4 Options The local MP2 reference wave function is produced through Pipek Mezey localization
253. e information in the file for these calculations the file should contain this line CALCULATION TYPE 02 followed by information for LMP2 wavefunctions 10 6 1 Describing Bonding Types in the Lewis File The bonding type information for HF DFT or GVB wavefunctions 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 informa tion for the first atom should follow immediately after the BONDING TYPE 01 label The first character 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 Jaguar 5 5 User Manual 255 Chapter 10 Other Jaguar Files with no leading spaces and must contain information for bond orders 1 2 and 3 with 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
254. e keywords select is printed Many of the print options can be turned on from the GUI as described in Section 6 4 on page 124 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 9 21 on page 187 causes the virial ratio V T to be printed out at the end of each SCF calculation Table 9 31 Output Keywords and Their Settings 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 ips 2 Memory disk and i o information ip6 2 Timing information user CPU and user system CPU 204 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 31 Output Keywords and Their Settings Cont d Keyword Value Description 2 ip7 2 ip8 2 ip11 2 3 4 5 ip12 2 ip13 2 ip18 2 ip19 2 ip23 2 ip24 2 ip25 2 ip26 2 ip70 2 ip170 2 ip173 2 ip192 2 3 ip193 2 ip194 2 Jaguar 5 5 User Manual Timing information user cpu and wall clock Grid shell locations Gaussian function list for derivatives of basis functions Bond lengths and angles Same as setting ip11 2 but includes all internuclear distances regardless of connectivity and torsion
255. e moment resulting from the fitted charges is generally similar to that calculated from the wavefunction 7 2 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 complete you can usually find the new input file by following the directions at the end of this section A new input file or restart file appears in the local job directory when any Jaguar job is completed This 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 wavefunction the final geometry and the like Thus if you want to restart the calculation with the wavefunc tion 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
256. e of using a dynamic constraint on a variable 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 particular 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 opti mizer 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 9 4 on page 166 5 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 reactant and product geometries To set up a transition state search open the Optimization window and select transition state search from the Optimization task option menu The Transition state search window is displayed You should use this window to describe the sort of transition state optimization you want to perform then return to the Optimization
257. e 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 coef ficients 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 provides 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 246 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files 10 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 dafv0300 5 6 lt number of sets atom number of rows set 3 0 5 0 7 0 9 0 lt neighbors cutoffs distances neighbors row 2 BASIS 6 31G 1 10 2 H 0 040634 0 080953 0 161278 0 321306 0 640122 1 275283 2 540684 5 061679 10 084136 1 100000 fro C X X X Se re a Oc O00 NY WwW OOO W OW QVO Ce e i OO FP OL o uD SS Seo oa x Se a oO lo codo C C NJ ON OC CORRKRO DG OO or a
258. e the Edit Input window 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 Methods window If you calculate the Hessian as part of the IRC or MEP calculation symmetry is turned off in the Hessian eval uation and remains off for the remainder of the run The direction of the reaction coordinate is not defined by the transition state on its own You can specify the reactant structure by setting Geometry 2 and the product structure by setting Geometry 3 in the Structure dialog box You must specify both or neither See Section 5 3 2 on page 90 for information on setting these geometries The default calculation generates 6 points in both forward and backward directions from the supplied transition state 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 incorporated 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 the Jaguar Quick Start Guide For information on keywords for IRC calculations see Section 9 5 10 on page 185 34 Keyword irc 2 in gen section of input file 35 Keyword irc 1 in gen section of input file 36 Keyword ircmode both in gen section of input file Jaguar 5 5
259. e 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 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 ultrafine 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 9 5 25 Plotting Keywords You can generate a plot file using keywords in the gen section that contains the values of the 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 molecular surfaces The length units for the grid are set with the iunit keyword The possible values of the plotting keywords are given in Table 9 40 An alternative to using these keywords
260. e the Pair slider To set RCI on for all pairs choose RCI on for all pairs from the RCI pair selection option menu The RCI for this pair button is dimmed but is automatically on for all pairs 4 4 GVB LMP2 Calculations 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 18 28 If you were editing an input file directly instead of using the GUI you would need to set GVB pairs in the gvb section of the input file Jaguar 5 5 User Manual 57 Chapter 4 Options For GVB LMP2 calculations Jaguar first performs an SCF calculation of the reference GVB wavefunction using the GVB pairs specified in the input Next the program applies an LMP 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 first specify the GVB pairs to be used in the GVB reference wavefunction following the procedure described in Section 4 3 on page 56 Next request an LMP2 treatment on all pairs in the system by choosing LMP2 all pairs from the Pairs option menu in the Local MP2 window You can perform the LMP2 calcula tion at either the valence only or the all electrons level We advise using GVB LMP2 primarily for single point en
261. 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 9 34 For example ip106 10 would mean that all orbitals were to be printed in FORTRAN f8 5 format after the GVB initial guess was created The options ip105 12 are not valid use ip100 instead In canonical orbital space the atom and function type labels are mean ingless If a keyword is set to 4 5 9 or 10 the results are suitable for input in the guess section or for input to GAUSSIAN 92 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 or XX for d are shown When ipx 4 n or ipx 5 n all coefficients are listed in order but without numbering Jaguar 5 5 User Manual 200 Chapter 9 The Jaguar Input File For examples of the output that shows up in the output file for a calculation o
262. ealiasing 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 func tion centered on the other atom The dealiasing functions themselves are simple polynomials multiplied by Gaussian func tions and are s type p type and so on depending on the polynomial Uncontracted dealiasing functions are simply formed by specifying the exponent of the Gaussian func tion 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 uncon tracted 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 contraction coefficients and exponents are desired Section 10 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 calcu lation Comments about a sample file refer to the sample daf file in Sectio
263. ecause the van der Waals radii are adjusted according to the chemical structure found by Jaguar and for generating an improved initial guess for transition metal containing systems along with the multip keyword See Section 7 1 1 on page 139 for more information on using this improved initial guess method The esp keyword can be used to tell Jaguar 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 TSEL esp column entry for an atom is set to n or no or 0 the atom will not be included in charge fitting If the esp column entry for a 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 inconsistent 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 220 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File on the restart file for which the charge fitting grid has been altered to include points around the dummy atom s by including a grid
264. ecente tenen 15 2 8 Shortcut Key CombiInatoDis roe erben reo bett n creep assess 16 2 0 Updoins dn OpBeratioli essre nn A ree Porra EE er ER Ies 17 2 10 Maestra Command SCFIDIS cione iter etie rte dere reet Pere eo e ER Eo rb coveave reds 17 2 11 Specifying a Maestro Working Directory sese 18 2 12 Running and Monitoring Jobs aios 19 2313 Help naso de De er RETO Rd CORDON ERU 20 2 14 Ending a Maestro SessIOD ero e e eere rir er ee i tette e PReU 21 Chapter 3 Running Jaguar From Maestro eee eese e esee ee eren eene tne een 23 3 1 Sample Calculatton 2 eat peteret eere dee Ure rere orale 23 3 2 Molecular Str eture Input eere eter rte ae tpe petet erret 26 3 2 1 Entering or Editing a Geometry Using the GUI 26 3 2 2 Cartesian Format for Geometry Input sssini nss 28 3 2 3 Variables in Cartesian Input esie reet retener aeree rete tud 28 3 2 4 Constraining Cartesian Coordinates esse 29 3 2 5 Z Matrix Format for Geometry Input eesesseeene 29 3 2 6 Variables and Dummy Atoms in Z Matrix Input ess 31 3 2 7 Constraining Z Matrix Bond Lengths or Angles 32 3 2 8 Counterpoise Calculations rte treten 32 3 2 9 Specifying Coordinates for Hessian Refinement s 32 3 3 Charge nd Multiplicity State a etre nei eter eter eme
265. ection 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 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 convergence 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 jumpal 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 Jaguar 5 5 User Manual 233 Chapter 9 The Jaguar Input File Note that since loops will only exit when convergence is reached the program before a goto or jump label must have such a criterion The three programs which can precede a goto or jump label are scf 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
266. ed Constraints Bond Lengths Bond Angles Torsional Angles OK Cancel Help Figure 5 1 The Geometry Optimization window 5 1 2 Geometry Convergence Issues 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 wavefunction is considered converged when the root mean squared 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 Methods window whose button appears in the Jaguar panel For the initial iterations of an optimization the SCF calculations are performed at the quick accuracy level described in Section 4 9 5 on page 78 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 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
267. ed in Section 9 5 22 on page 208 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 1s 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 14 228 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 9 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 speci
268. efault for solvation calculations 2 Fit electrostatic potential to atomic centers and bond midpoints incdip 0 Use only total charge as constraint in electrostatic potential fit ting 1 Use charge and dipole moment as constraints in electrostatic potential ESP fitting 11 Use charge dipole moment and quadrupole moment as con straints in electrostatic potential ESP fitting 188 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 23 Integer valued Keywords for Charge Fitting Multipole Moment and Polarizability amp Hyperpolarizability Calculations Cont d Keyword Value Description 111 Use charge dipole moment quadrupole moment and octapole moment as constraints in electrostatic potential ESP fitting ijk Compute ESP fitted charges using total charge as a constraint also constraining to dipole moment if k 1 to quadrupole moment if j 1 and to octapole moment if i 1 1 Do all incdip options sequentially Idips 1 Do not calculate any multipole moments 2 Calculate dipole moments 3 Calculate dipole and quadrupole moments 4 Calculate dipole quadrupole and octapole moments 5 Calculate dipole quadrupole octapole and hexadecapole moments ipolar 0 Do not calculate polarizabilities or hyperpolarizabilities 2 Calculate polarizabilities and first and second hyperpolarizabil ities B and y using CPHF method 1 Calculate polarizabilities and hyperpolarizabilities B using CPHF method 1 Calculate pola
269. el 68 Jaguar 5 5 User Manual Chapter 4 Options 4 7 5 Infrared Intensities To calculate infrared intensities for each frequency in km mol select IR Intensities For HF jobs where frequencies are calculated analytically the IR intensities are obtained from coupled perturbed Hartree Fock CPHF calculations of the derivative of the dipole moment with respect to changes in the nuclear coordinates and molecular symmetry is not used for the job For calculations for which frequencies are computed numerically the numerical derivative of the dipole can be obtained for IR intensity calculations Analytic IR intensities are not available for open shell molecules 4 7 6 Thermochemical Properties Thermochemistry calculations of a system s constant volume heat capacity C internal energy U entropy S enthalpy H and Gibbs free energy G at standard temperature and pressure are performed by default whenever vibrational frequencies are calculated Rotational symmetry 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 By using the thermochemistry settings you can control the temperatures and pressure used for calculations of these quantities The pressure in atm used for thermochemical calculations is 1 0 by default and the initial temp
270. elevant effective core potential information If symmetry is turned off that setting will be entered into the 992 file For GVB calculations you should specify GVB pairs Jaguar will also generate a GVB initial guess which will be included in the g92 file For more information on setting up GAUSSIAN 92 input files see Section 7 3 on page 143 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 gt Gaussian 92 basis set gbs If this option is turned on a gbs file will be generated containing the basis set in a form that can be used by GAUSSIAN 92 XYZ file xyz If you set this option Jaguar creates a file in XYZ format with the suffix xyz The file contains all geometries generated during the course of the job except that for solvated geometry optimizations the file only contains the solvated structures 13 Keyword ip160 2 in gen section of input file 14 Keyword ip168 2 in gen section of input file 15 Keyword ip165 3 in gen section of inp
271. ence options unless you are having convergence problems You might want to select the wave function type or the electronic state 4 9 1 Wavefunction Type Restricted or Unrestricted To perform an unrestricted HF or DFT calculation you can select Unrestricted UHF UDFT from the Wavefunction type option menu The default method for open shell systems is restricted open shell HF or DFT 66 65 Keyword iuhf 1 in gen section of input file 66 Keyword iuhf 0 in gen section of input file 74 Jaguar 5 5 User Manual Chapter 4 Options Methods Wavefunction type Restricted ROHF RODFT Electronic states Ground state r tiianbor of elactranic states h HF initial guess Automatic d GVB initial quess lt BF initial guess l Convergence scheme Maximum iterations Energy convergence RMS density matrix change SCF level shift Accuracy level quick Analytic Corrections Standard Corrections Final localization off zd Symmetry off Symmetry populations not fixed OK Help Figure 4 9 The Methods window 4 9 2 Selecting Electronic States To perform a configuration interaction singles CIS calculation to obtain information on excited electronic states choose Excited States from the Electronic States list and enter the number of excited states for which you want information in the Number of Electronic States text box When you select a CIS calculation Jaguar first p
272. ence schemes 11 104 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 20 although it is generally much slower than DIIS You can change the maximum number of SCF iterations allowed 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 The default energy convergence criterion for Jaguar 9 which can also be changed is set to 5 0 x 10 Hartrees for the total energy on consecutive iterations except for polarizability calculations for which it is 1 0 x 10 Hartrees If the energy difference is less than 1 of the previous energy difference however this convergence criterion is overridden for that iteration and the calculation continues When the RMS change in density matrix elements for a polarizability hyperpolarizability or geometry optimization calculation is less than the RMS density matrix element change criterion whose default value is 5 0 x 10 the calculation is considered to have converged For polarizability and hyperpolarizability calculat
273. ener ally 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 5 5 User Manual 137 Chapter 6 Output 138 Jaguar 5 5 User Manual Chapter 7 Tips and Suggestions This chapter includes information on restarting jobs and using Maestro to help set up GAUSSIAN 9x jobs as well as some extra suggestions for GVB calculations geometry optimization electrostatic potential fitting and jobs involving transition metals 7 1 Tips for Various Types of Jobs This section contains information you may find useful for improving SCF convergence running GVB jobs and optimizations and fitting charges 7 1 Organometallics and Other Difficult to Converge Systems Generally Hartree Fock wavefunctions 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
274. energy structure or tran sition state are performed at the LMP2 level the program der1b never runs Instead forces are calculated by the programs 1mp2der 1mp2gda 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 If Optimize geometry is set to minimum energy or transition state 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 5 2 on page 86 the constraints are also listed in the pre output At the end of the first SCF calculation the programs der1a rwr and der1b run calcu lating the forces felt by each atom in the unoptimized geometry and writing 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 optimiza tion 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
275. ented FON fractional occupation number and pFON pseudo FON In the first method FON the Fermi energy is determined so that the resulting occupations sum to the total number of electrons In the second method pFON 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 value 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 though use of symmetry is recommended and it can be used with the ipopsym keyword Jaguar 5 5 User Manual 197 Chapter 9 The Jaguar Input File 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 func tion 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 calculation if their eigenvalues are less than cut20 It may be necessary
276. enting it If you continue to have this problem and it is affecting the GUI performance you should ask your system administrator for help 12 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 only 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 Temp directory setting in the Jaguar Run window The program actu ally 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 Temp directory listing of scr erwin for a job called h2o with an input file called h20 in 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 Run window exists and that you have write permission within that directory For example if
277. ents for Jaguar and whether they are met Display a command syntax summary including a list of valid commands Jaguar 5 5 User Manual 267 Chapter 11 Running Jobs The job control functions of the jaguar command jobs kill stop and purge 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 11 1 you can use the jaguar command with the options listed in Table 11 2 to obtain information about Jaguar versions and hosts available Some of these options can be qualified by arguments that limit or define the list of versions displayed These version arguments are listed in Table 11 3 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 Note The options listed in Table 11 2 and Table 11 3 apply to all Schr dinger programs not just to Jaguar Table 11 2 Information Options for the jaguar Command Option Description WHICH version args Show which version of jaguar and of the mmshare library would be used for the given version args LIST version args List the available versions of Jaguar that can be run on the s
278. eopt dft II bat geopt dft III bat j2 bat pka bat pka_2input bat pka_deprot bat OK Cancel Help Figure 3 8 The Select Batch Script window The default selection in the Select Batch Script window is the built in JOBS bat script The Notes window shows comments from the JOBS bat script As they indicate this script simply runs a series of jobs from the input files it is passed By default the built in scripts directory is selected To select one of the other directories listed above choose User scripts or Local scripts from the option menu in the middle of the window 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 3 1 Table 3 1 Description of Built in Batch Scripts Script Description JOBS bat geopt DFT I bat geopt DFT II bat geopt DFT III bat 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 j2 bat Run a J2 theory calculation 25 pka bat Run a pKa calculation See Chapter 14 for details 42 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Jaguar batc
279. er account name on that host by listing the file name in the format host fullpath or user 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 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 9 5 23 on page 210 Comments in the input file are ignored by Jaguar If an input file was produced using the GUI text entered in the box marked Comment in the Run or Save window generally appears on the fourth line of the input file If the geometry was symmetrized as described in Section 3 5 2 on page 37 a comment indicating the point group to which it was symme trized appears 9 1 1 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 at all we suggest that you use equals signs between a keyword and its value and avoid using them
280. er hosts file is being used by clicking the About button in the Jaguar panel then clicking the Schr dinger button in the About window The schrodinger hosts file currently used by Jaguar is listed near the bottom of the window Jaguar 5 5 User Manual 263 Chapter 11 Running Jobs If you want to change entries in the schrodinger hosts file you should copy and edit your own schrodinger hosts file If there is no schrodinger hosts file in your SHOME schrodinger directory or the directory from which you start Maestro you should identify the schrodinger hosts configuration file currently used by Maestro copy this schrodinger hosts file to your HOME schrodinger directory or the directory where you want to start Maestro and edit it there The following is an example of a schrodinger hosts file Schrodinger hosts file name localhost schrodinger software schrodinger name ahost name bhost name old_bhost host bhost schrodinger software schrodinger_old name another_host processors 2 tmpdir scr schrodinger usr bin share schrodinger End of Schrodinger hosts file The hosts file consists of one or more entries that describe a host on which jobs can be run Typically there will be a single entry for each machine on which you want to run jobs For each entry in the schrodinger hosts file the following settings can be made name entry label host machine name user userid tmpdir
281. er1b 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 stop ping optimization maximum number of iterations reached depending on whether the convergence criteria were met before the maximum number of iterations was reached 6 3 6 Optimizations With GVB RCI Wavefunctions Geometry or transition state optimizations using GVB RCI run in much the same way as described above for HF GVB or DFT optimizations except that the forces for the optimi zation are computed numerically rather than analytically Consequently the der1a and derib programs never run instead when forces are needed the structure s energy is evaluated at 6N tom perturbed geometries where N tom is the number of atoms and the forces are computed numerically The program nude generates each perturbed geometry by moving an atom a small amount in the positive or negative x y or z direction and also evaluates the numerical derivatives when calculations on all perturbed geometries are complete listing them in a force table similar to the usual geometry optimization force table described for HF GVB or DFT systems The program geopt still runs in the usual way as well computing each iteration s new geometry using the available forces 6 3 7 Solvation Performing a solvation calculation involves several iterations in which the wave functions fo
282. erature in K is 298 15 by default Either of these settings can be changed To compute thermochemical properties at more than one temperature specify the differences between temperatures using the Temp Incre ment setting and the number of temperatures at which thermochemical properties should be computed with the Number of steps setting which is 1 by default By default thermochemical output is in units of kcal mol for H and G and cal mol K for C and S To report the output in units of kJ mol and J mol K instead select J mol from the Output units menu 58 Keyword irder 1 in gen section of input file 59 Keyword press in gen section of input file 60 Keyword tmpini in gen section of input file 61 Keyword tmpstp in gen section of input file 62 Keyword ntemp in gen section of input file 63 Keyword ip28 2 in gen section of input file Jaguar 5 5 User Manual 69 Chapter 4 Options name gu iat zal L2 Molecular stoichiometry C6H6 120 basis functions used for 6 31 G OK Cancel Help Figure 4 8 The Basis Set window 4 8 Basis Set From the Basis Set window you can choose a basis set 4 from the option menu shown under the label name and select polarization and diffuse functions from the option menus marked and respectively If an option 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
283. erforms a closed shell Hartree Fock calculation The Hartree Fock orbitals are used as input to the CIS calcula tion You cannot do a CIS calculation based on an open shell SCF wavefunction The output includes excitation energies transition dipole moments and oscillator strengths from the ground state to the excited states 67 Keyword icis 1 in gen section of input file 68 Keyword nroot in gen section of input file Jaguar 5 5 User Manual 75 Chapter 4 Options 4 9 3 Choosing an Initial Guess Type The default HF initial guess selection is Automatic meaning that Jaguar selects the initial guess method most likely to lead to convergence However you can explicitly select from among several possible initial guess algorithms By default for non GVB calculations on simple closed shell systems with no transition metals Jaguar constructs the initial wavefunction from orbitals that give the best overlap with previously calculated orbitals from atomic calculations This initial guess method which can be selected for any calculation is identified as AO Overlap The algorithm used is described in reference 14 This method compares well with the semi empirical schemes that other ab initio programs use to obtain initial guesses Jaguar also provides a unique initial guess feature to improve SCF convergence both HF and DFT particularly for transition metal containing systems As described in reference 19 research at Schr dinger ha
284. ergies within about 0 1 kcal mole of results from all analytical integral calculations 12 The internal contraction 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 deter minants The GVB RCI program within Jaguar generates a correlated wavefunction from intra pair excitations of the GVB reference wavefunction described in Section 8 2 using a highly effective 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 Jaguar 5 5 User Manual 153 Chapter 8 Theory The spatial states for an RCI pair are constructed from the same natural orbitals as those used for the GVB reference wavefunction y and but in addition to the GVB spatial state from Equation 6 rewritten here 2 2 Spo CpgV pg Cpu pu 14a the RCI spatial states include the orthogonal complements m and o2 Spl V pgW pu 14b 2 2 Ep2 Cpu pg CpgW pu 14c Just as the GVB method allows the user to correlate particular electron pairs for maximal efficiency the RCI treatment can be applied to a
285. ergy 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 change the basis set in the restart file to cc pWTZ f and restart the job See Section 7 2 on page 142 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 The most effective choice of GVB reference wavefunction depends on the type of calcula tion being performed For conformational energy calculations we recommend setting all possible GVB lone pairs all possible GVB pairs that describe multiple bonds between two carbons and all GVB pairs for bonds between two different non hydrogen atoms For information on how to make these GVB pair settings automatically see Section 9 5 5 on page 170 For studies of bond dissociation all bonds from the atoms involved in the dissociating bond or bonds should be treated at the GVB LMP2 level Note also that for dissociation of multiple bonds GVB LMP2 s accuracy is limited by its inadequate treat ment of spin coupling between high spin fragments we recommend using the GVB RCI method instead for such cases 4 5 Solvation Jaguar can treat solvated molecular systems with a self consistent reaction field method using its own Poisson Boltzmann solver 15 135 You can compute solvation energies and minimum energy solvated s
286. ergy 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 labels 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 114 Jaguar 5 5 User Manual Chapter 6 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 iter ation 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 solu tion 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
287. ess 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 or the gvb section if you are comparing GVB results to HF LMP2 or DFT results A substitution of a specified number or character string for one already in the tem plate input file The format for each of these options and an example of each kind are shown in Table 11 7 Option assignments must not 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 characters lt gt in a substitution pattern These options and the other line types in a batch input file are illustrated in the sample files in the next subsection After the examples directions on how to submit a batch job follow in the final subsection Table 11 7 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 set dftname b3lyp ting igeopt NONE specify a data file path filetype fullpathname or file BASISFILE usr es my bas and
288. est in Directories Files benzene dft 01 in 35 benzene dft 01 plot in 3rdbenzeneretest prj benzene dft in Qui ckTopi cs2 prj benzene hf 01 in methy amine_pka benzene_hf in benzene_mp2 01 in benzene_mp2 in methylamine in E IL a File Format Jaguar input Read as Geometry and settings Selection oT Figure 3 4 The Read File window 3 4 Reading in Geometries and Job Settings The only file types for which Jaguar can read any calculation information besides the geometry and molecular charge are Jaguar input files GAUSSIAN 92 23 input files and BIOGRAF 21 Hessian files To read calculation information choose Geometry and settings from the Read as option menu Geometries and settings read in from a Jaguar or GAUSSIAN 92 input file are displayed in the GUI Settings that do not have GUI controls are read in even if they are not displayed 3 4 3 Read as Geometry 2 or Geometry 3 Settings In the Read File window two options in the Read as option menu Geometry 2 and Geom etry 3 are designed for input only for certain types of transition state optimizations These options are described in Section 5 3 on page 88 which explains special options for transi tion state optimizations Jaguar 5 5 User Manual 35 Chapter 3 Running Jaguar From Maestro 3 5 Cleaning up Molecular Geometries The molecular geometry sometimes needs improvement before you perform calculations For example it might not h
289. etie e dre 50 41 2 DEF Model OPONE tinis ttr ee ene trita ee en ene mre Perte re reste 51 4 1 3 Custom Punctionals cep eor Ben UR i 53 4 2 Local MP2 Settt bs epe HPIHE entere ER Es RE Le tee a ENEE EE 54 4 2 1 Summary of the LMP2 Method in Jaguar sees 54 4 2 2 Setting up an LMP2 Calculation rere teres 55 4 3 Generalized Valence Bond GVB Settings esee 56 4 3 1 GVB or GVB RCLI Pair Inp t rre einer 57 44 GNVB ENMP2 Calculatiags 5 eoo vedeen rone sah setts vaveses sonst rt Herten goa 57 A SEV cim 58 45 1 Solvent Parameters eee ea feries eo RA 59 4 5 2 Performing or Skipping a Gas Phase Optimization 60 46 Properties ette ien e eU eer He ERI EORR FREE RR LEER E 60 4 6 1 Electrostatic Potential Fitting nire retten intent 60 4 6 2 Multipole MORIS ooa t set ee oreet Eee eret eite reet 62 4 6 3 Polarizability and Hyperpolarizability eese 62 4 6 4 Electron Density eene rettet eden trn eret eren get aatas heroine 63 Jaguar 5 5 User Manual Contents 4 6 5 Mulliken Population Analysis eerte tetti ettet nnde 64 4 6 6 Natural Bond Orbital NBO Analysis eene 64 4 7 Exequencies and Related Properties 2 ae eret emeret 64 4 T I Prequencle8 ueterem e terere Fer Etpa Uo rere rhe 65 ATZ Atomie UELLE 66 4 7 3 Scaling Of Prequencies 5 eene trier ene teet beton
290. f water with a 6 31G basis set for various values of ip104 see the five examples given at the end of Section 6 7 on page 133 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 9 5 23 Grid and Dealiasing Function Keywords The grid and dealiasing function keywords allow the user to select from among the various sets of grids and dealiasing functions available in the grid and dealiasing grid and da input files which are described in Section 10 3 on page 243 and Section 10 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 gdft grad 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
291. fferent software installations You can also use the name and host settings to specify a batch queue name and the host on which the batch system is available The host name does not need to include the full Internet address unless the host on which you plan to run the calculation host is not on the same local network as the host from which you plan to submit jobs the submission host The value 1ocalhost is a special name setting that means the host from which the job was submitted In addition to this function the localhost entry sets the default values of settings for all other entries In the schrodinger hosts file example above the host entries ahost and bhost inherit the schrodinger setting from the localhost entry 11 1 2 The user Setting If you have different user IDs on the submission and calculation hosts you must include a user setting for the calculation host in the schrodinger hosts file on the submission host This schrodinger hosts file must be a local copy 11 1 3 The tmpdir Setting The tmpdir setting specifies a directory where scratch directories can be created such as scr or temp From this setting Jaguar creates a scratch directory named tmpdir userid jobname to store temporary files where userid is your account name on the calcu lation host and jobname is the name of the Jaguar job For example if the user erwin ran a job named h2o on the host withi using the schrodinger hosts file above the temporary direc
292. fog display state 4 Enhance depth cues Displays a menu from which you Q Q m Optimizes fogging and other depth cues choose an item Automatic means on a based on what is in the Workspace when there are more than 40 atoms in the Workspace off when there are fewer 12 Jaguar 5 5 User Manual Rotate around X axis by 90 degrees Tile entries Arranges entries in a rectangular grid in the Workspace Save view Saves the current view of the Work space orientation location zoom Display only this molecule Picks the molecule to display Double click to display all atoms Also display Displays a menu from which you can select a category of atoms to add to the display or open the Atom Selection dialog box to select atoms to add to the display Display atoms within N angstroms of currently displayed atoms Displays a menu from which you can select a value or open a dialog box to enter a value The value selected is per sistent Display ribbon atoms only Displays protein atoms used to define ribbons Draw bonds in wire representation Double click to apply to all bonds Draw atoms in Ball amp Stick represen tation Double click to apply to all atoms Color all atoms by scheme Displays a menu from which you can choose the scheme Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface wA eT II e Q Q KI Rotate around Y axis by 90 degrees Reset Workspace Resets the rotation trans
293. for GAUSSIAN 9x Users We recognize that some Jaguar users also use GAUSSIAN 9x for calculations Therefore Jaguar can generate or read GAUSSIAN 9x input files If you plan to perform GVB calcula tions with GAUSSIAN 9x you may find this feature particularly useful since you can use Jaguar to generate a high quality GVB initial guess automatically 7 3 1 Generating GAUSSIAN 9x Input Files With Jaguar You can use the GUI as a convenient tool to create GAUSSIAN 9x input files The output file that is produced from the Jaguar run and whose name ends in g92 can be used as a GAUSSIAN 9x input file The 992 file requests an HF or ROHF restricted open shell Hartree Fock calculation whichever is appropriate for the number of electrons in the Jaguar 5 5 User Manual 143 Chapter 7 Tips and Suggestions system unless you choose to specify another method Details applying only to constructing an input file for a GVB calculation are discussed below To create a g92 file turn on the Gaussian 92 input deck g92 option in the File Output window whose button appears in the Output section of the Jaguar panel If you are just creating a GAUSSIAN Ox input file and you do not want to use Jaguar to generate a converged wavefunction you can save some time by using the Edit Job window to add the keyword setting igonly 1 initial guess only to the gen section of the input file The information in the g92 file depends on the information you have provi
294. formation on the hosts to the job control facility through a file named schrodinger hosts How to provide this information is described in the next section 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 subse quent section 11 1 Customizing Host Configurations The installation directory SCHRODINGER contains a file named schrodinger hosts that identifies hosts on which Jaguar can be run and provides some information about the use of the host When you start Maestro the settings in the schrodinger hosts file are used to determine the available options in the Jaguar Run window You can copy and edit the schrodinger hosts file to customize its settings You shouldn t need to update any schrodinger hosts files when you later install other versions of Jaguar Information on the schrodinger hosts file is given in the Schr dinger Product Installation Guide and includes instructions for batch queue config uration No information on batch queue configuration is given in this chapter Maestro searches the following directories for a schrodinger hosts file in the order given and uses the first one that it finds The directory in which you started Maestro SHOME schrodinger SSCHRODINGER You can always determine which schroding
295. 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 11 3 on page 275 for details on jaguar batch commands including command line options Jaguar 5 5 User Manual 81 Chapter 4 Options 82 Jaguar 5 5 User Manual Chapter 5 Optimizations and Scans For Hartree Fock GVB LMP2 and DFT calculations in gas phase or in solution Jaguar can use calculated analytic gradients to optimize the molecular geometry to a minimum energy structure or a transition state while for GVB RCI calculations optimizations can be performed using numerical forces 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 3 9 3 on page 46 5 1 Geometry Optimization The Basics The Geometry Optimization window contains the settings for optimization of minimum energy structures or transition states The Optimization task is set to none by default meaning that Jaguar performs a single point calculation The energy minimization option requests a search for the molecular geometry
296. fy a certain number of the lowest eigenvectors of the Hessian for refinement as described in Section 5 3 6 on page 92 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 slightly and uses the results to refine the initial Hessian to be used for the optimization 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 if you type either of the following two input geometries in the Edit Geometry window O1 H2 O1 i q H3 O1 i T1 H2 108 0 or O1 H2 O1 ohbond H3 O1 ohbond H2 108 0 ohbond 1 1 they will have the same effect a job from either input that includes Hessian refinement will use both O H bonds and the H O H angle in the refinement Molecular symmetry or the use of variables either of which may constrain several coordi nate values to be equal to each other can reduce the number of coordinates actually used for refinement For example for the second water input example shown above only two coordinates are actually 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 3 3 Ch
297. fying the point charge in atomic units and the next three specifying its x y z coordinates in the same units used for the geometry angstroms by default but bohr if the iunit keyword in the gen section is set to 0 or 2 see Section 9 5 1 on page 168 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 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 9 12 The efields Section If you would like to calculate wavefunctions 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 compo nents of the electric field should be specified in atomic units on the same line The requested properties 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 the elec
298. g for GVB pair natural Orbitals 0 dee 108 GBV RCI theory sese 153 connect input file section 166 connectivity keyword for bonding output keyword output option seen consecutive Jaguar jobs running from Maestro 40 44 running with jaguar batch 275 280 Jaguar 5 5 User Manual constraints for geometry optimization 29 32 86 87 166 keywords for esee 181 constraints dynamic eee 167 convergence criteria geometry optimization 84 85 111 183 SCF energy SCF energy keyword for solvation energy keyword for 188 convergence problems troubleshooting 287 convergence schemes eeeeeeee TI DIIS tie titt T1 123 keywords for nere 194 OCBSE 2 d 123 coord input file section eee 166 coordinates Cartesian in geometry input 28 constraining and freezing 86 for refinement of Hessian 32 Coulomb corrections sees 254 Coulomb field charge fitting to 117 Coulomb operator J contributions to energy keyword for output obtaining i o information for 125 pseudospectral assembly of 148 149 counterpoise calcu
299. g type information If the Lewis file contained the bonding type information example provided in Section 10 6 1 which included the lines Jaguar 5 5 User Manual 259 Chapter 10 Other Jaguar Files Table 10 3 Lewis File Hybridization Numbers and Corresponding Hybridization Types Hybridization Corresponding Number Hybridization Type 1 s hybridization 2 p hybridization 3 d hybridization 5 sp hybridization 6 sp hybridization 7 sp hybridization 8 sp d hybridization 9 sp d hybridization 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 information 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 would mean that this radius information line 6 1 120 1 1 1 2 00 C in H2 C C or H2 C O 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
300. h PA 1992 Babel version 1 6 copyright 1992 96 W Patrick Walters and Matthew T Stahl All Rights Reserved Permission of authors granted to incorporate Babel into Jaguar Jaguar 5 5 User Manual 25 26 21 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 References Dunietz B D Murphy R B Friesner R A Calculation of enthalpies of forma tion by a multi configurational localized perturbation theory application for closed shell cases J Chem Phys 1999 110 1921 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 F Frisch M J J Phys Chem 1994 98 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 Wilk 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 VWN5 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
301. h orbitals are then truncated to a local space built from the atomic basis functions on the local atomic centers orthogonalized to the occupied space Another crit ical advantage 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 corre lated 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 45 However localized MP2 implementations in conven tional 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 local ization 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 effi ciency of the pseudospectral implementation of LMP2 as detailed in ref 16 In the pseu dospectral 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 p
302. h scripts can either require that you specify an input file or list of input files to be run with the recipe in the batch file or they can include a self contained list of Jaguar input files The information in the kind of script is displayed in the middle of the Select Batch Script window If the script you select processes input files select an input file or list of files 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 avail able from the Inputs option menu in the Jaguar Batch window If you choose Use current structure from workspace or Use currently selected project entries the structures are written to a single Maestro file and the Jaguar input files are created later by the batch facility The file name can be set in the Name text box in this section of the window To select pre existing files choose Use selected disk files from the Inputs menu then click Select input files The Select Batch Inputs window is displayed with the current directory and its files listed You can enter a directory in the Input Dir text box When you press RETURN the names of the available input files are displayed in the Files list You can select either Jaguar input files or Maestro files for input If you select Maestro files Jaguar input files are constructed later You can control whether Maestro mae files and Jaguar resta
303. h 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 Jaguar 5 5 User Manual 245 Chapter 10 Other Jaguar Files each contracted function These integers dictate how to construct the actual functions from the exponents just given in the daf file for uncontracted functions and already estab lished 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 func tion 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 rele vant 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 exponents were listed earlier and the contracted functions corresponding to the contracted
304. he elec tron density calculation and the total number of electrons found over the grid The main Jaguar 5 5 User Manual 119 Chapter 6 Output output file does not include the charges and grid points for the calculation that informa tion 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 elec tron density in au respectively for each grid point If you calculate Mulliken populations by atom the charge for each atom and the sum of the atomic charges will be noted under the heading Atomic charges from Mulliken popu lation analysis If you choose to calculate them by basis function the atomic charge output will be preceded by a section labeled Mulliken population for basis functions listing the atom label function labeled with consecutive numbers type of basis function S for s X for p XX for d etc and calculated population Calculating Mulliken popu lations by bond yields the populations by atom and basis function as well An example of this output for a calculation of water using the 6 31G basis set is provided below Mulliken Bond Populations first nearest neighbor Atoml Atom2 Pop Atoml Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop H1 Oo 0 314 H2 Oo 0 314 Mulliken Bond Populations second nearest neighbor Atoml Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop Atomli Atom2 Pop H2 H1 0 025 Mu
305. he first line in the effective core potential description contains the element symbol e g Na and two numbers The first of these indicates the maximum angular component in the core and the second indicates the number of electrons replaced by the effective core potential Next the information for various angular components is listed The first set of such information contains the local components of the ECP and should begin with a line saying D AND UP F AND UP or G AND UP which indicates that the maximum angular components to be described are 2 3 or 4 respectively Following that line the different terms for this angular component are given Each line describes a term of the form Ce 97 2 listing the parameters n a and C from left to right in a free format Next the lower angular components 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 def ault 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 which 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 11 10 0 497200000000000 0 275357400000000 5 6000
306. he heading Jaguar NBO 5 0 6 3 10 Frequency IR Intensity and Thermochemistry Output If you calculate vibrational frequencies by making the appropriate setting in the Frequen cies window any SCF calculations during the run use the RMS density change conver gence criterion described in Section 4 9 on page 74 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed for several more iterations than single point energy calculations yield To compute the Hessian for vibrational frequencies Jaguar calculates the second deriva tives either analytically or numerically as the derivatives of the analytical first derivatives depending on the type of calculation see Section 4 7 on page 64 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 hf ig grid rwr scf derla rwr and der1b run setting up and performing SCF calculations and evaluating analytic gradients at 6N perturbed geometries unless the number of perturbed geometries needed is reduced by the use of molecular symmetry To make each perturbed geometry one atom is moved a small fixed amount in the positive or negative direction along the x y or z Cartesian axes After the calculations at the perturbed geometry Jaguar performs one final calculation at the unper turbed geome
307. he last entry in the range To select or deselect an entry without affecting the selection of other entries hold down the CTRL key and click the entry Simi Jarly to include or exclude individual entries or a range of entries from the Workspace use the SHIFT and CTRL keys in combination with mouse clicks Once you have selected project entries you can manipulate them using tools available from the Selection menu Clicking the right mouse button while the pointer is positioned over the Project Table so long as there is at least one entry in the table displays the Selec tion menu at the mouse position You can use the mouse to perform operations besides selecting entries Clicking and drag ging with the middle mouse button on the boundary of a row resizes that row Clicking on selected entries and dragging allows you to reposition the entry in the Project Table The entries are placed after the first unselected entry that precedes the entry on which the cursor is resting when you release the mouse button For example if you select entries 2 4 and 6 and release the mouse button on entry 3 these three entries are placed after entry 1 because entry 1 is the first unselected entry that precedes entry 3 To move entries to the top of the table drag them above the top of the table to move entries to the end of the table drag them below the end of the table Jaguar 5 5 User Manual 15 Chapter 2 The Maestro Graphical User Interface A summa
308. here is the output for a calculation of water s dipole and quadrupole moments 116 Jaguar 5 5 User Manual Chapter 6 Output Moments from quantum mechanical wavefunction 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 2Z2Z 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 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 of the output from such a calculation for water follows dummy atom x4 is between 2 and 1 dummy atom x5 is between 3 and T angstroms atom x y z Oo
309. his 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 a 1 it indicates a polarization function which is included in the basis set if the basis set name ends in a as described in Section 4 8 on page 70 If the number is a 2 it indicates a basis set function if 1 a basis set function 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 de ault basis infor mation generally follows this rule although there are some exceptions see the Li s and p function information 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 num
310. hylbenzylamine 9 2 9 5 0 3 hexamethylenetetramine 6 3 5 3 1 0 DABCO 9 5 8 2 1 3 ANILINES aniline 4 6 4 6 0 0 4 chloroaniline 3 9 4 0 0 1 4 methoxyaniline 5 4 5 2 0 2 4 nitroaniline 0 9 1 0 0 1 p toluidine 4 5 5 1 0 6 312 Jaguar 5 5 User Manual Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group Chapter 14 The pKa Prediction Module MOLECULE pKa calc pKa exp Deviation AMIDINES imidazo 2 3 b thioxazole 8 2 8 0 0 2 tetrahydrozoline 10 0 10 5 0 5 hydroxyimidazo 2 3 a isoindole 9 1 8 6 0 5 tolazoline 10 6 10 3 0 3 HETEROCYCLES 2 aminopyridine 7 2 6 7 0 5 2 aminothiazole 5 7 5 4 0 3 2 methylimidazole 8 0 8 0 0 0 3 aminopyridine 6 1 6 0 0 1 4 aminopyridine 9 7 9 7 0 0 4 methylpyridine 6 2 6 0 0 2 benzimidazole 5 3 5 8 0 5 imidazole 6 9 7 0 0 1 isoquinoline 5 5 5 4 0 1 melamine 5 0 5 0 0 0 pyrazine 1 2 0 7 0 5 pyrazole 2 5 2 5 0 0 pyridine 5 3 5 3 0 0 pyrimidine 1 1 1 3 0 2 quinoline 5 0 4 8 0 2 thiazole 2 6 2 8 0 2 BENZODIAZEPINES 1 3 dihydro 1 methyl 5 phenyl 1 4 benzodiazepin 3 7 3 3 0 4 2 one 1 3 dihydro 3 hydroxy 5 phenyl 1 4 benzodiaz 2 0 1 7 0 3 epin 2 one Jaguar 5 5 User Manual 313 Chapter 14 The pKa Prediction Module Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group MOLECULE pKa calc pKa exp Deviation 1 3 dihydro 3 hydroxy 1 methyl 5 phenyl 1 4 ben 1 4 1 6 0 2 zodiazepin 2 one 1 3 dihydro 5 phenyl 1 4 benzodia
311. iables can be set up by root in the default environ ment or they can be set up in a login script to avoid having to set them manually at each session The last strategy does not work for ksh which does not execute a login script The mpi ch 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 13 1 and the available options are listed in Table 13 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 You can override this default by specifying a file in the SCHRODINGER NODEFILE environment variable or by using the m option The port on which the servers listen can be specified using the p option or the MPI PASSPORT envi ronment variable otherwise the standard port number 1234 is used Jaguar 5 5 User Manual 293 Chapter 13 Parallel Jaguar Table 13 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 config
312. ibed is composed of that number of primitive Gaussians 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 For instance 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 two in the next two rows The jcont values of 1 in the next five rows indicate that the primitive Gaussians being described are components in a contracted function whose first primitive Gaussian term is listed in the first row The values in the column marked ishl take on nonzero values when basis functions corresponding to different values as described in the next column use primitive Gauss jans with the same exponents Positive values indicate that the same exponents should be used in the shell listed that number of rows down a value of 1 indicates that the expo nents should be provided from a shell listed earlier The values in the next column indi cate 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 one less than the lowest number corresponding to the basis function or functions being described For example the nfsh 2 entries below are for p functions so the f
313. ical keywords for 184 formal charge see 220 fragments defining iisconeiedeee petentis 225 frequencies for 193 226 fred proram inet ente te eese 233 frequencies 65 66 fragment eines 193 226 keywords for 184 192 SCAMS irri eere 66 67 visualizing in Maestro 67 visualizing with Molden 66 Frequencies window 64 69 output from sese 121 123 frequency related properties keywords for 5 5 ree eee 191 OULDULa ire eie te teer 121 123 SOU SS TOL rent tiit rts 69 functionals see density functional theory DFT G GAMESS input files key wotd for io one etes 207 OptOn foireann terere 130 gas phase optimizations option to skip 60 GAUSSIAN 92 Hessian format sess orbital output in format for GAUSSIAN 92 basis set file gbs keyword for generation of 145 207 option for generation of 130 333 Index GAUSSIAN 92 input file 992 keyword for generation of 144 207 option for generation of 130 143 145 reading sss 34 35 145 286 Gaussian function list in output keywords i 204 gen input file section 168 generalized gradient approximation 139 Generalized Valence B
314. ich 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 the cutoffs 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 accu racy problems but increases the computational cost by a factor of two to three For more information on grids and cutoffs see Section 10 4 on page 248 and Section 10 5 on page 252 4 9 6 Analytic Corrections For efficiency Jaguar uses both numerical and analytical methods The trade off is that analytic methods are more accurate but also more time consuming Setting analytic corrections to Fully analytic calc results in a non pseudospectral calculation which is significantly slower than the usual method The default is Standard Corrections for which the exact number and type of analytically calculated two electron integrals 105 106 are automatically determined 82 Keyword vshift in gen section of input file 83 Keyword iacc 3 in gen section of input file 84 Keyword iacc 2 in gen section of input file 85 Keyword iacc 1 in gen section of input file 86 Keyword nops 1 in gen section of input file 87 Keywords noatcor 0 and nops 0 in gen section of input file 78 Jaguar 5 5 User Manual Chapter
315. id and the keyword ipltunit sets the units of length The possible values of the keywords are given in Table 9 47 Table 9 47 Plot Section Keywords Keyword Value Meaning iorbla 3 Generate electrostatic potential data 2 Generate density data 1 Generate data for all alpha orbitals 0 Do not generate any plot data gt 0 Index of first alpha orbital for data generation iorb2a gt 0 Index of last alpha orbital for data generation Ignored unless iorbla is positive 234 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 47 Plot Section Keywords Cont d Keyword Value Meaning iorblb 1 Generate data for all beta orbitals 0 Do not generate any plot data for beta orbitals gt 0 Index of first beta orbital for data generation Ignored for restricted wave functions iorb2b gt 0 Index of last beta orbital for data generation Ignored unless iorb1b is positive npts nx ny nz Number of points in each Cartesian direction The three values can be separated by commas or spaces origin Ox Oy Oz Coordinates of box origin The three values can be separated by commas or spaces extentx X Y Z Coordinates relative to the origin of the maximum extent of the box in the x direction Only x should be nonzero extenty X Y Z Coordinates relative to the origin of the maximum extent of the box in the y direction Only y should be nonzero extentz X Y Z Coordinates relative to the origin of the maximum extent of the bo
316. if the energy change is less than 2 5 x 10 The symbol following each quantity used to judge convergence indicates how well converged it is The symbol indicates convergence criteria that are not satisfied indicates criteria that are satisfied indicates criteria that are quite well satisfied indicates values that are essentially zero If the convergence criteria mentioned are not met and if the maximum number of iterations has not been exceeded the output notes molecular structure not yet converged and the optimization continues Jaguar 5 5 User Manual 111 Chapter 6 Output 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 the 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 optimization 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 d
317. ificantly higher level of theory than the geometry optimization however 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 extensive 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 We use the cc pVTZ basis set of Dunning and coworkers in the present methodology The cc pVTZ basis set repre sents a mixed basis set where cc pVTZ is used for atoms involved in the deprotona tion 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 sub stituents 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 com puted 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 trea
318. ign flip ping or reverting to an older Hessian 118 1 Before using Hessian to update geometry modify it by RFO rational function optimization level shifting 123 Default for geometry optimizations that do not use dynamic constraints 2 Before using Hessian to update geometry modify it by P RFO partitioned rational function optimization level shifting 123 Default for transition state searches Automatically set for geom etry optimizations that use dynamic constraints ifollow 0 For each transition state optimization iteration select a new eigenvector to follow 1 For each optimization iteration follow eigenvector that most closely correlates with one followed previously 182 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 17 Integer Keywords for Geometry and Transition State Optimizations Cont d Keyword Value Description itrvec 0 For transition state optimization select lowest Hessian eigenvec tor as transition vector gt 0 Select eigenvector number itrvec as transition vector see Section 5 3 on page 88 Sets ifollow to 1 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 itradj 0 Use same trust radius throughout optimization default for mini mum energy structure optimizations 1 Adjust trust radius using Culot Fletcher heuristic 122 124
319. ilar correction terms are computed for the exchange operator as detailed in ref 13 The corresponding pseudospectral terms as defined by Equation 3a and Equation 3b for the appropriate choices of i j k and l 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 8 2 Pseudospectral Implementation of the GVB Method The pseudospectral method has also been extended to electron correlation methods with a particular focus on Generalized Valence Bond GVB 20 calculations Highly refined GVB initial guess 14 and convergence 11 algorithms have been automated within Jaguar allowing the scaling advantages resulting from the pseudospectral method to be maintained for GVB calculations The method yields very accurate excitation energies rotational barriers and bond energies for many molecules 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 thu
320. ile If you click OK the unrecog nized information is retained in the input for the job and could cause your job to fail 3 9 4 The About and Help Buttons The About button displays information about Jaguar and Schr dinger You must close the window before using other parts of the GUI The Help button opens the Help window You can see on line help on a variety of subjects by clicking on them as they are listed under the Help items heading so that they show up in the Selection bar then clicking Select You can also obtain help for any window by Jaguar 5 5 User Manual 47 Chapter 3 Running Jaguar From Maestro clicking the Help button The Help window appears with the appropriate topic selected All of the information in the on line help is also included in this manual 3 9 5 Closing the Jaguar Panel Clicking Hide hides or closes the Jaguar panel Hiding the panel merely means that it is hidden from view none of the settings are lost and jobs started from the panel continue to run 3 9 6 Other Jaguar Panel Options Most of the settings that control the choice of method or theoretical model are described in the next chapter The Output buttons for requesting additional information in output files are described in Chapter 6 48 Jaguar 5 5 User Manual Chapter 4 Options You can make many of the calculation settings for Jaguar jobs using the windows that are opened by clicking on the following buttons in the Jaguar panel
321. im Acta 1973 28 213 Hehre W J Ditchfield 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 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 Jaguar 5 5 User Manual 325 References 84 85 86 87 88 89 90 9 92 93 94 95 96 97 98 99 100 101 102 103 104 326 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 95 1358 Woon D E Dunning T H Jr J Chem Phys 1994 100 2975 Easton R E Giesen D J Welch A Cramer C J Truhlar D G Theor Chim Acta 1996 93 281 Schafer A Huber C Ahlrichs R J
322. imply 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 convergence scheme uses Fock matrices from all previous iterations for the run and Fock matrices are not stored in new input files However calculations should ulti mately 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 Jaguar Run window 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 geom etry optimizations as well as at the end of each SCF iteration To turn off restart in file generation the input file output keywords ip151 and or ip152 in the gen section would need to be set to 0 The restart in file overwrites itself each time so that the final version is written either at the end of the run or just prior to any problems encountered 7 3 Suggestions
323. in etuer d aere ce 218 226 atomic section cssssee 218 226 atomic units 164 165 In Output 4n rrr mo eto cetee 125 keyword for geometry input 168 229 atomig file default ences nes 237 description and format 242 243 specifying in input file 161 Au to Help nene feeds 20 319 B babel using to convert file formats 201 204 using to read input files 34 Balloon Help sess 20 319 basgss basis set label 227 228 basis file description and format 237 241 specifying in input file 161 basis functions contracted senesini 126 127 derivatives of list in output 205 file containing eee 237 241 for individual atoms 221 in counterpoise calculations 32 keyword for printing 204 listing in output 121 Mulliken populations for 120 number of 102 243 Dini 126 129 type as listed in output 120 134 209 uncontracted suus 126 127 basis input type eese 221 Basis set sisirin at 70 74 conversion to Jaguar format 241 diffuse functions 70 71 193 238 file containing 237 241 for individual atoms 221
324. in the gen section of the input file for the frequency calculation These settings are made in addition to any other frequency related settings 9 5 14 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 4 3 on page 71 or Table 4 4 on page 73 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 4 8 on page 70 Neither polarization nor diffuse functions are used if none of these options are specified The tables in Section 4 8 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 set automatically depending on the basis set as described in Section 4 8 Possible settings for numd are shown in Table 9 26 Table 9 26 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 9 5 1
325. ine Entry Points Degree Reference for Grid 6 18 5 Un 5 1 Albrecht amp Collatz p 294 129 7 24 5 Un 5 4 Stroud p 295 129 8 26 7 Un 7 1 Albrecht amp Collatz p 295 129 9 38 9 9 1 Lebedev 130 10 38 9 9 1 Lebedev 130 11 42 9 9 2 Lebedev 130 12 44 9 9 3 Lebedev 130 13 44 9 9 4 Lebedev 130 14 50 11 U3 11 1 McLaren p 301 129 11 1 Lebedev 130 15 54 11 11 2 Lebedev 130 16 56 11 U3 11 2 Stroud p 301 129 17 60 11 11 3 Lebedev 130 18 60 11 11 3 Lebedev 130 19 78 13 13 2 Lebedev 130 20 78 13 13 3 Lebedev 130 21 86 15 15 1 Lebedev 130 22 90 15 15 2 Lebedev 130 23 90 15 15 2 Lebedev 130 24 110 17 17 1 Lebedev 130 25 116 17 17 2 Lebedev 130 26 146 19 19 Lebedev 131 27 146 19 19 Lebedev 131 28 194 23 23 Lebedev 131 29 302 29 29 Lebedev 132 30 434 35 Lebedev 133 Jaguar 5 5 User Manual 251 Chapter 10 Other Jaguar Files 10 5 The Cutoff File The cutoff file specifies parameters to be used for the various iterations of an SCF calcula tion The file to be used is determined by the CUTOFFFILE entry in the input file as described in Section 9 1 on page 161 If the input file has no such line 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
326. inement would use both O H bonds and the H O H angle in the refinement Molecular symmetry or the use of variables either of which may constrain several coordi nate values to be equal to each other can reduce the number of coordinates actually used for refinement For instance for the water input example shown above only two coordi nates will actually 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 geome tries see Section 5 3 on page 88 for details For these jobs you can input the second and or 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 zmat section Alternatively if the changing coordinates 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 geometries See Section 9 3 for details Jaguar 5 5 User Manual 165 Chapter 9 The Jaguar Input File 9 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
327. ing file names for input and output displaying molecular geometries symmetrizing geometries and setting run time parame ters such as the machine that will perform the calculation We suggest you start by trying the sample calculation in Section 3 1 If the calculation runs successfully you 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 12 Chapters 4 and 5 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 4 includes information on using generalized valence bond GVB restricted configuration interaction RCI Mgller Plesset second order perturbation theory and density functional theory DFT techniques calculating solvation energies vibrational frequencies hyperpolarizabilities multipole moments and other properties fitting charges specifying basis sets and various other options Chapter 5 describes optimiza tions of the molecular structure transition state searches and geometry scans Chapter 6 describes how to summarize Jaguar output and the output or printing options available 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
328. inger tmpdir scr processors 2 host marge schrodinger apps Schrodinger tmpdir scr processors 2 1 host bart schrodinger apps Schrodinger tmpdir scr processors 1 4 Ensure that rsh is enabled By default Jaguar uses rsh to communicate with remote nodes even if you are running on a stand alone SMP workstation with 2 CPUs To enable rsh each user must create a file called rhosts in his or her home directory The rhosts file should contain the name of each host listed in the file machines LINUX 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 writ able by anyone except the user or authentication fails To ensure this enter the command chmod 644 rhosts We strongly recommend that you test rsh connections by using the shell script tstmachines which is in MPICH install sbin This script attempts to run sev eral rsh commands on each of the hosts listed in the file machines LINUX and lists any problems If the command 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 Note Because MPICH uses rhosts authentication you must set up the rhosts file even if you are using ssh for communication 292 Jaguar 5 5 User Manual Chapter 13 Parallel Jaguar 13 1 2 3 Launching the Secur
329. ion number mmshare version number Maestro version number Operating system with version number 2 14 Ending a Maestro Session To end a Maestro session choose Quit from the Maestro menu To save a log file with a record of all operations performed in the current session click Quit save log file in the Quit panel This information can be useful to Schr dinger support staff when responding to any problem you report Jaguar 5 5 User Manual 21 Chapter 2 The Maestro Graphical User Interface 22 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro The Jaguar panel in the Maestro GUI can simplify the submission of jobs You can run the GUI and the Jaguar calculation on different machines In addition as with any X program the machine running the GUI the X client does not need to be the machine or terminal that displays the GUI the X server This means that from any X terminal or workstation running X you can log on to a machine where Maestro is installed and submit jobs on another machine on which the Jaguar executables are installed Without the GUI you would have to create input files with particular formats in order to run Jaguar The GUI creates these input files for you based on information you give it and submits the job This frees you from learning the input format and program sequences and instead allows you to concentrate on the science involved The GUI also provides a convenient method of incorporating
330. ions if the energy conver gence criterion described in the previous paragraph is satisfied first the calculation ends even if the RMS density matrix element change criterion has not been met and vice versa 75 Keyword ihfgvb 0 and iguess 1 in gen section of input file 76 Keyword iconv 1 in gen section of input file 77 Keyword iconv 4 in gen section of input file 78 Keyword iconv 3 in gen section of input file 79 Keyword maxit in gen section of input file 80 Keyword econv in gen section of input file 81 Keyword dconv in gen section of input file Jaguar 5 5 User Manual TI Chapter 4 Options The SCF level shift setting determines the amount that the energies of the virtual orbitals are increased before diagonalization in atomic units Level shifting reduces the mixing of the real and virtual orbitals which slows convergence but often helps otherwise intrac table cases to converge Useful SCF level shift values are generally in the range 0 3 1 0 4 9 5 Accuracy Level The grids used for various SCF iterations and the accuracy with which parts of the calcula tion are done greatly affect the timing and sometimes the accuracy of the entire calcula tion You can adjust the grids and the set of cutoff values determining these factors using the Accuracy level option menu The usual default quick setting allows fast calculations to be performed using several different pseudospectral grid types and cutoffs wh
331. ip165 When ip165 is 3 the SPARTAN 4 0 archive file is written to the local job directory as jobname arc When ip160 equals 3 an initial guess is included in the g92 file generated by the run by default g92 files generated for GVB calculations include initial guesses but those for other calculations do not If SCF iterations are performed the initial guess for the 992 file will be obtained from the resulting wavefunction otherwise it will be generated from the appropriate Jaguar initial guess routine When ip160 equals 5 the basis set is included explicitly within the g92 file rather than just the basis set name When it equals 4 the trial wave function and the basis set are included 206 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 32 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 992 file see text for ip160 3 4 or 5 ip163 GAUSSIAN 92 basis set gbs file ip164 MOQM 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 128 file resp file set to 3 to include grid weights ip175 XMol file xyz file with geometries generated during optimization ip177 AIMPAC
332. is computed Localiza tion can also be used to provide localized orbitals for the LMP2 method see Section 9 5 6 on page 172 for details The keywords in Table 9 29 describe the available options for final wavefunction localization See Section 4 9 7 on page 79 for a description of the localiza tion methods and the GUI settings related to localization Table 9 29 Keywords Related to Localization of Orbitals Keyword Value Description locpostc 0 Do not localize core orbitals of final wavefunction 1 Perform Boys localization on core orbitals of final wavefunction 2 Perform Pipek Mezey localization on core orbitals of final wave function maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on core orbitals of final wave function maximizing Mulliken basis function populations 1 Mix the core and valence orbitals before localization then local ize according to the locpostv setting locpostv 0 Do not localize valence orbitals of final wavefunction 1 Perform Boys localization on valence orbitals of final wavefunc tion 2 Perform Pipek Mezey localization on valence orbitals of final wavefunction maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on valence orbitals of final wavefunction 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 localization ixtrb
333. 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 STO3G STO 3 STO3 5D H S 0 2 1 1 0 3 42525091400000 0 154328967294599 0 623913729800000 0 535328142281266 0 168855404000000 0 444634542184440 KKKK He S 0 3 i 2 6 36242139400000 0 154328967291452 1 15892299900000 0 535328142270350 0 313649791500000 0 444634542175373 KKKK Li S 0 3 4 16 1195747500000 0 154328967293323 2 93620066300000 0 535328142276839 0 794650487000000 0 444634542180763 SP 0 1 2 i 15 70 0 636289746900000 9 996722918659862E 02 0 155916274998087 0 147860053300000 0 399512826086407 0 607683718592546 4 808867839999999E 02 0 700115468876179 0 391957393095192 ERER Basis sets containing effective core potentials ECPs are described in a slightly more complicated fashion First the string ECP must appear between the 5D or 6D label and the BACKUP label This string indicates that the basis set description contains information about the effective 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 Jaguar 5 5 User Manual 239 Chapter 10 Other Jaguar Files described above After a line with two asterisks the effective core potential is described T
334. isplay purposes To use a different grid for electron density calculations see Section 9 5 23 on page 210 for information about the grid keyword geldens in the gen section of the input file 42 Keyword ipolar 1 in gen section of input file 43 Keyword ipolar 5 in gen section of input file 44 Keywords Idens 1 and geldens 3 in gen section of input file 45 Keyword denspc in gen section of input file 46 Keywords Idens 1 and geldens 4 in gen section of input file Jaguar 5 5 User Manual 63 Chapter 4 Options 4 6 5 Mulliken Population Analysis Mulliken populations 58 can be computed for each atom giving a representation of the molecule as a set of nuclear centered point charges For open shell cases Mulliken spin populations 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 4 6 6 Natural Bond Orbital NBO Analysis To request a default Natural Bond Orbital NBO analysis 59 at the end of the Jaguar job turn on NBO analysis at the bottom of the Properties window The output from the NBO analysis is included in the Jaguar output file Othe
335. isurf should be 0 but the keyword ivanset should be 1 All Lewis dot keywords are explained in Section 9 5 5 on page 170 The radius settings in the file default lewis which appears in the standard data direc tory were optimized for HE GVB and LMP2 solvation calculations in water with Jaguar s solvation 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 134 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 262 Jaguar 5 5 User Manual Chapter 11 Running Jobs Running monitoring and controlling jobs is done by the Maestro 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 scratch 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 infor mation on job control can be found in the Maestro User Manual Some of this information is repeated here If you intend to run jobs on various hosts you must provide in
336. it 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 See Section 11 3 on page 275 for more information 11 2 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 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 5 5 U
337. it is not necessary to memorize the commands for every operation or to be familiar with the command language Simply perform the desired operations using the GUI controls copy the logged commands from the Command History list into the Script area of the panel and then save the list of copied commands as a script To run an existing command script open the Command Script Editor panel from the Edit menu in the main window Click Open Local and navigate to the directory containing the desired script Select a script in the Files list and then click Open The command script is loaded into the Script window of the Command Script Editor panel To execute the script click Run Script Command scripts cannot be used for Prime operations 2 11 Specifying a Maestro Working Directory When you use Maestro to launch Jaguar jobs Maestro writes job output to the directory specified in the Directory folder of the Preferences panel By default the directory to which Maestro writes files the file i o directory is the directory from which you launched Maestro To write the output files to another directory change the preferences as described below 18 Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface Preferences prefer Sex Delete Markers Font size Project Directory Label Mouse File Suffix Default directory for job startup and file i o Maestro s current working directory ww Parent of project directory w
338. ital generated by the earlier operations After all manipulations 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 Q k 1 p end hfiglcmob p q Y r s 0 amp 9 15 The echo Section The echo section when it is included in input files does not contain anything but its own label amp echo amp Its purpose is to signal Jaguar to include a copy echo of the input file in the output file If your input file does not contain an echo section the output file will not contain an echo of the input file 9 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 acces sible from the executable directory you must specify the full path for that program with a character at the beginning of the path Table 9 46 gives a brief description of each Jaguar program Jaguar 5 5 User Manual 231 Chapter 9 The Jaguar Input File Table 9 46 Individual Programs Included in Jaguar
339. itial Hessian Tof 32 33 92 93 165 166 182 MIPS scesstie ates tvs acs ie dures 141 142 transition states 88 troubleshooting sse 287 trust radius 85 86 183 184 188 updating of Hessian 182 options effect on output file 106 Jaguar 5 5 User Manual Index orbital energies IN O tput ih erid iii 105 output option eeeeeereree 131 orbitals combining eee 230 231 information in output 103 104 107 keywords for output of 208 210 output options oo eee 133 136 plotting sss 79 81 234 236 printing for guess section 228 reordering eei 230 231 orbman input file section 230 order of Jaguar programs run SPECTEYIN E MR 231 234 ordering of dealiasing functions 245 organometallics improving convergence o 76 139 141 output file comments in echoing input file in effect of calculation options on Content iiec general description location reference in log file standard output settings 124 129 summarizing ener 97 102 output file information BASIS 123 convergence methods other than DIIS 123 DFT calculation options 106 frequency IR and thermochemistry Calculatio
340. ive diagonalization of the Hamiltonian to obtain the RCI coefficients The Davidson method is used for this step Jaguar 5 5 User Manual 155 Chapter 8 Theory 8 4 Pseudospectral Local MP2 Techniques Second order Mgller 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 conformational energies However the scaling of conventional MP2 algo rithms with system size is formally nN where N is the number of basis functions and n the number of occupied orbitals due to the necessity of carrying out a four index transfor mation 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 correlation effects on observable quanti ties Thus MP2 techniques have traditionally been used primarily for small molecules Several years ago Pulay and coworkers 43 44 formulated a version of MP2 in which the occupied orbitals are first localized e g via Boys localization 46 and the virtual space correlating suc
341. l are listed first followed by the atoms described by the alternate 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 All ECP basis sets use five d functions as described earlier in this section Currently the LACVP LAV3P and LACV3P basis sets use the pseudospectral method while all other ECP basis sets use the analytic method computing the four center two electron integrals explicitly 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 functions 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 4 9 Methods The Methods window includes various settings that control the type of calculation and how the calculation is performed including the wave function type the electronic states the source of the initial wave function the convergence method the maximum number of SCF iterations and the job s accuracy level You should not need to change the conver g
342. l angles during an optimization Jaguar will then keep these coordinates unchanged throughout the job To freeze all coordinates of a particular type first open the Geometry Optimization window To make Constraints settings from this window you must first choose energy minimization or transition state search from the Optimization task option menu You can then turn any of the constraint settings for Bond Lengths Bond Angles or Torsional Angles using the buttons at the bottom of the Optimization window 5 2 2 Freezing Specific Coordinates You can constrain freeze specific coordinates in your geometry input to remain fixed at their original values during an optimization From the Edit Geometry or Edit Job window you can freeze a specific coordinate by adding a sign at the end of its value in your geometry input For example to fix the HOH bond angle of water at 106 0 you could use the following Z matrix 15 Keyword nooptr 1 in gen section of input file 16 Keyword noopta 1 in gen section of input file 17 Keyword nooptt 1 in gen section of input file 18 The geometry input including constraints signs is in the zmat section of the input file 86 Jaguar 5 5 User Manual Chapter 5 Optimizations and Scans Oo H1 O 0 9428 H2 O 0 9428 H1 106 0 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 variab
343. l control keywords including those describing the calculation per formed the grids dealiasing functions and cutoff parameters used the electro static 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 or delocalization of LMP2 pairs atomic Sets atom specific properties including atomic masses for isotopes van der Waals radii for solvation calculations and basis functions for individual atoms hess Allows input of initial nuclear Hessian guess Allows input of initial wavefunction 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 plot Allows data to be generated for plotting of orbital potential or densities nbo Requests NBO Natural Bond Orbital calculation Each section is delineated by a pair of amp or characters The section name follows immediately 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
344. l 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 converted 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 10 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 const
345. l surface for each entry To run other calculations using the same input file after running a surface calculation clear the settings in the Calculate Surfaces window then click Don t Run to reset the input file settings and close the window without running a job 4 11 J2 Theory Calculations If you want to calculate energies accurately you can perform J2 theory calculations 25 using a predefined batch script The J2 batch script performs a B3LYP 6 31G geometry optimization and frequency calculation followed by single point GVB LMP 2 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 parameter ized 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 frequen cies The J2 results do not include a standard heat of formation because the relevant calcu lations for the constituent atoms are not made To run J2 theory calculations first create and save an input file containing the desired molecular geometry In the Jaguar Batch window click the Select button and select the script j2 bat from the list of built in scripts Then select the input file or files from the list in the Jaguar Batch window and click RUN The J2 job is run on the local host You can also use the jaguar j2 command to run the calculation
346. lation and zoom of the Workspace to the default state Restore view Restores the last saved view of the Workspace orientation location zoom Display only Displays a menu from which you can select a category of atoms to display or open the Atom Selection dialog box to select atoms to display Undisplay Displays a menu from which you can select a category of atoms to undisplay or open the Atom Selection dialog box to select atoms to undisplay Display ribbons only Displays ribbons for protein atoms Display both ribbons and atoms Displays ribbons along with the protein atoms used to define them Draw atoms in CPK representation Double click to apply to all atoms Draw bonds in tube representation Double click to apply to all bonds Color by constant color Displays a menu from which you can choose the color The color choice is persistent You can then pick molecules to apply the color or double click the button to apply the color to all atoms 13 Chapter 2 The Maestro Graphical User Interface Label atoms Displays a menu from which you can choose a single type of label to apply to all atoms Display H bonds Displays a menu from which you can choose to display H bonds within the selected molecule intra or between the selected molecule and all other atoms in the Workspace inter The choice is per Label picked atoms Displays a menu from which you can choose a pick state open the Atom Selecti
347. lations 32 165 defining fragments for 225 specifying atoms for 221 coupled perturbed Hartree Fock CPHF terms for LMP2 dipole moments 54 62 for LMP2 ESP fitted charges 54 61 coupled perturbed Hartree Fock see CPHF calculations covalent radii eere 221 CPHF calculations of hyperpolarizability 63 189 of polarizability 63 189 cpolar program seeseeeee 232 GPU UT sies rtr nee tnter e ea 204 Culot Fletcher method for trust radius adjustment keyword for 183 current working directory default me setting in Maestro CUTOFF fleri oi default coiere merece Jaguar 5 5 User Manual Index specifying in input file 161 cutoff methods suues 78 84 195 CUtOffS iid cedere crore 195 196 252 253 shown in output 105 157 D daf file default tritt bieten en 237 description and format 243 248 neighbor ranges 243 244 specifying in input file 161 dealiasing functions 71 243 choices for calculation 244 contracted ssuss 244 245 246 keyword for list in output 204 keywords eese 210 211 long range
348. lculation are specified This information is followed by the molecular geometry input 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 geom etry which is used for the rest of the calculation One electron integrals are calculated by the onee program which prints the smallest eigenvalue of the overlap matrix S and the number of canonical orbitals used for the calcu 102 Jaguar 5 5 User Manual Chapter 6 Output lation Canonical orbital eigenvectors with very small eigenvalues less than 5 0 x 104 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 wavefunction initial guess for a Hartree Fock calculation The output from the program hfig for a default calculation begins with the line
349. le 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 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 Cartesian coordinate list For example if your input for an optimization of a water mole cule looked like this Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 the H atoms would only be allowed to move within the xy plane in which they started If frozen Cartesian coordinates are included in the input for an optimization Jaguar uses Cartesian coordinates for the optimization rather than generating redundant internal coor dinates and the optimization does not make use of molecular symmetry 5 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 coordi nates 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 forma
350. le in the geometry input as described in Section 3 2 on page 26 then set the variable using one of the options above For instance to vary the angle HCCH over the values 0 30 60 90 120 150 180 you could set it with 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 the at 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 the innermost on the 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 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 For each geometry in the scan the default initial guess is taken from the previous geom etry You can change this behavior using the igscan keyword in the gen section of the input file 94 Jaguar 5 5 User Manual Chapter 5 Optimizations and Scans 5 5 Intrinsic Reaction
351. lectrostatic potential ESP to a set of point charges 55 56 These monopoles can be located either at the atomic centers or at the atomic centers and the bond midpoints depending on the Fit ESP to selection The atomic charges are 32 Keyword nogas 0 in gen section of input file 33 Keyword nogas 2 in gen section of input file 34 Keyword icfit 1 in gen section of input file 35 Keyword icfit 2 in gen section of input file 60 Jaguar 5 5 User Manual Chapter 4 Options Fit ESP to atom centers m ESP constraints total charge only r ESP grid type spherical ESP wid spacin Multipole moments none d Polarizability Hyperpolarizability t field atomic tais Electron density on grid Density grii spacing Mulliken populations NBO analysis off OK Cancel Help Figure 4 5 The Properties window 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 For electrostatic potential fitting of an LMP2 wavefunction 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 may also want to constrain the charge fitting to reproduce the dipole moment as described below Because the CPHF term is computationally expensive it is not included in LMP2 charge fitting by
352. lliken population for basis functions atom func type population Oo 1 S 1 9954 Oo 2 S 0 8942 Oo 3 X 0 8034 Oo 4 Y 0 9514 Oo b Z 1 1426 Oo 6 S 0 8865 Oo 7 X 0 4669 Oo 8 Y 0 6649 Oo 9 Z 0 8332 Oo 10 XX 0 0085 Oo 11 YY 0 0024 Oo 12 ZZ 0 0052 Oo 13 XY 0 0142 Oo 14 XZ 0 0000 Oo 15 YZ 0 0021 H1 16 S 0 4950 H1 17 S 0 1263 H1 18 X 0 0185 H1 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 120 Jaguar 5 5 User Manual Chapter 6 Output Atom O 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 from the Standard window whose button appears under the Output heading if you want to have more information about the basis functions More information on this output option is given in Section 6 4 on page 124 If both Mulliken populations and multipole moments are calculated the multipole moments are calculated from the atomic Mulliken populations as well as directly from the wavefunction as noted in Section 4 6 5 on page 64 The output lists the multipole moments from the wavefunction 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 Output for NBO calculations appears under t
353. luated over grid points g as follows Kj M OA jag rg 22 g where Q is the least squares fitting operator for molecular orbital i on grid point g R is the physical space representation of virtual orbital p and A is the three center one elec tron integral 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 Aug described in Equation 2 by A jag 2 cuc Ang 23 The summation is performed in two steps first summing over k to form intermediates A A jig dure 24 k then summing over to yield the integrals in molecular orbital space jqg 2 0 i 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 13 158 Jaguar 5 5 User Manual Chapter 8 Theory 8 5 Density Functional Theory Density functional theory DFT is based on the Hohenberg Kohn theorem 110 which states that the exact energy of a system can be expressed as a functional depending only on the electron density In the Kohn Sham implementation of DFT 111 this density is expressed in terms of Kohn Sham orbitals occ p 2 w r 26 similarly to the density expression used for Hartree Fock SCF calculations For simplicity we consider only closed shell syste
354. luster For computer clusters that do use queuing software host entries must be included for each queue that is to be used and value of processors for each entry should be the total number of processors available in the cluster See Section 11 1 on page 263 for details of the format for the schrodinger hosts file For all platforms you should use local disks for scratch space Performance is signifi cantly reduced if an NFS mounted scratch disk is used Also avoid using scratch directo ries which are actually symbolic links Using symbolic links for scratch directories is known to prevent Jaguar jobs from running especially under Linux Thus if scratchis actually a symbolic link to scr specify scr in the schrodinger hosts file rather than scratch 13 1 1 SGI Installation There are two system requirements for SGI a version of Message Passing Toolkit MPT no earlier than 1 2 1 1 and a version of Array Services no earlier than 3 1 If you are using the PBS batch queue system you will need a version of MPT no earlier than 1 5 0 0 These packages must be installed by the system administrator for your computer because the installation requires root permission Following are installation instructions 1 Check to see if the required MPI Message Passing Interface files are already installed with the command showprods grep MPI If MPI is not installed you can install it from the MPT package which can be downloaded from http www
355. lvation 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 Localized 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 isoxazolone and Julolidinyl n N N diethylthiobarbituric acid Chem Phys Lett 1995 242 543 Murphy R B Pollard W T Friesner R A Pseudospectral localized generalized Meller 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 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 Pittsburg
356. ly constrained in zmat section 1 Constrain freeze all torsional angles for optimization 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 Jaguar 5 5 User Manual 181 Chapter 9 The Jaguar Input File Table 9 17 Integer Keywords for Geometry and Transition State Optimizations Cont d Keyword Value Description 2 Use Cartesian input Hessian found in hess section inhess 2 automatically if non empty hess section exists 4 Compute and use quantum mechanical Hessian irefhup 2 Refine initial Hessian using Powell updates 119 3 Refine initial Hessian using mixed Murtagh Sargent Powell updates 120 4 Refine initial Hessian using Murtagh Sargent updates 121 nhesref gt 0 Number of lowest frequency Hessian eigenvectors used in Hes sian refinement default is 0 ihuptyp 0 Don t update Hessian 1 Update Hessian each iteration using BFGS Broyden Fletcher Goldfarb Shanno method 122 default for minimum energy structure optimizations 2 Update Hessian using Powell method 119 3 Update Hessian using mixed Murtagh Sargent Powell method 120 default for transition state optimizations 4 Update Hessian using Murtagh Sargent method 121 not rec ommended 1 Compute quantum mechanical Hessian at each geometry sets inhess 4 irfo 0 Before using Hessian to update geometry modify it by s
357. m 0 65 to 9 17 Our empirical corrections take the simple linear form pK a pK 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 302 Jaguar 5 5 User Manual Chapter 14 The pKa Prediction Module neutral species The linear term takes into account the significant variation in charge on the ionizable 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 substituents such as in oxalic acid are replaced by electron donating substit uents such as in propionic acid This change in charge alters the hydrogen bonding first shell correction term as well as the solvation free energy computed by the SCRF calcula tion 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 correc tions there are also intrinsic errors in the gas phase DFT calculations which are implicitly incorporated 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 relative energetic changes produced
358. m pairs for local LMP2 calculations 55 56 172 205 hfug progra wisi csi sede sat Ceteri output from hybrid methods DFT hybridization types describing in Lewis EE A E T 256 hyperpolarizability keywords for 189 190 QUUDUL ees 118 selection of options for 62 63 I in file see input file infrared intensities sssss 69 192 tops e 123 initial guess choosing type eene file information for for restarted calculations 76 for transition metal systems 76 139 141 GVB from HF wave function 199 Improving eerie ors 139 141 information in output 103 input file section for 227 228 keywords for 198 199 orbital output in format for 135 209 output of GVB 132 208 printing orbitals after 133 209 stopping after oo eects 144 198 335 Index T put file bee te 161 236 comments in 40 162 comments on symmetrizing 38 defining fragments 225 226 description of sections 162 164 difeCtOry scatet teet ere eet 44 echoing in output eee 231 echoing in output file 124 editing ecrit ies tes 237 editing in Maestro 46 47 PEW SECON a uie etos 145
359. menu bar Workspace maestro zonet juliem est projects Maestro version 5 0 008 Maestro Project Edit Display Applications MacroModel Analys c r Ez gt X Be MES Q o ey EUER 9 9J xyz v Toolbar 2 JE l Top View n 3l Q j l 4 Viewing LIE volume indicators Sequence viewer Status bar Command input area Clipping plane Figure 2 1 The Maestro main window 6 Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface 2 2 The Maestro Main Window The Maestro main window is shown in Figure 2 1 on page 6 This window is composed of the title bar the Auto Help window the main menu bar the Workspace the top view area the toolbar the command input area and the status bar You can display any of the last five of these using the Display menu The functions of the main window components are as follows Title bar displays the project name and current working directory Auto Help automatically displays context sensitive help Main menu bar provides access to panels via pull down menus Workspace displays molecular structures Top view displays Workspace structures as viewed from above Toolbar contains shortcuts for many menu items and also tools for structure dis play and manipulation and organization of the Workspace Status bar displays the number of atoms entries residues chains and molecules currently displayed in the Workspa
360. metry is assumed to have as indicated in Table 9 2 Table 9 2 Options for the Keyword iunit Keyword Value Description iunit 0 Geometry units are bohr and radians Geometry units are Angstroms and degrees N Geometry units are bohr and degrees W Geometry units are Angstroms and radians 168 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 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 covfac times the sum of their covalent radii which are listed in Table 9 44 The default value for this variable is 1 2 9 5 2 Molecular State Keywords Charge and Multiplicity The keywords that describe the input molecule s charge and spin multiplicity are shown in Table 9 3 These keywords correspond to GUI options described in Section 3 3 on page 33 Table 9 3 Keywords to Describe the Molecular State Keyword Value Description molchg any Overall charge on molecule excluding point charges set in pointch section default 0 multi gt 0 Spin multiplicity 1 for singlet 2 for doublet etc default 1 p P plicity g except for ihamtyp 0 when multip 2 by default 9 5 3 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 9 8 on page 218 The masses used are from ref 118 Table 9 4 Keywor
361. mp but the following syntax is not supported amp atomic atom basis Cl 6 31g atom basis C1 cc pVTZ amp To print an atomic section in the job s 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 a job s input file the atomic section is echoed in the output from the program pre Jaguar 5 5 User Manual 219 Chapter 9 The Jaguar Input File 9 8 3 Keywords That Specify Physical Properties The keywords that specify physical properties of atoms are listed and defined in Table 9 41 Values for these keywords can appear in restart files Table 9 41 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 for charge fitting vdw2 van der Waals radii in A for solvation cov Covalent radius in A used to determine bonding and other properties The formal keyword is useful for solvation jobs b
362. ms in this overview of the method The Kohn Sham orbitals are expressed as a linear combination of basis functions r and the 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 y ri ja Eees qm a of xclP VPI F V Quen o where f p Vp is an exchange correlation functional and yis Vp Vp The exchange correlation functional f p Vp is usually separated into exchange and correlation functional components that are local or non local in the density fxclP Vp f lP f wr Ip Vol 28 St lp PY m ui le Vel Under the local density approximation LDA the non local functionals f vr IP VP and f y p Vp are ignored when either or both of these terms are included the gener alized 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 4 1 on page 49 and its references Jaguar 5 5 User Manual 159 Chapter 8 Theory The electronic ground state energy E is given by E 23 4rvi 5V v Jer V Gp Q9 arzt Jer f p Vp in Hartree atomi
363. mv old filename new filename to rename a file In that case you can input the path section in such a way that each line is assumed to contain a single command To input the path this way you must include the word line after the amp path or path label at the beginning of the path section 9 17 The plot Section The plot section allows you to generate data for one or more orbitals the potential or the density in a form that allows you to plot one of these properties on a cubic grid In order to request this data you must include a plot section with settings to describe what to plot the dimensions of the box in which it is to be plotted and the number of points in each direc tion in the box Since the plot section requests a plot of information from the initial guess unless a guess section is included in the input file you should use a restart file resulting from a completed job if you want to plot final properties from a job See Section 7 2 on page 142 for information on restart files You can also generate plot data using gen section keywords See Section 9 5 25 on page 214 for information on this option The plot section should contain settings for iorbla npts origin extentx extenty and extentz and may also contain a setting for iorb2a iorb1b iorb2b and ipltunit The keywords iorbla iorb2a iorb1b and iorb2b control the data that is generated the keywords npts origin extentx extenty and extentz define the gr
364. n amp coord C1 C2 Cl C2 C3 C1 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 optimization and the C1 C2 C3 C4 torsion You can also 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 As a simple example of the use of a dynamic constraint consider the following zmat section for a water molecule in which the distance between the two hydrogen atoms is 1 507 angstroms amp zmat o hi o 0 95 h2 o 0 95 hi 105 amp Now suppose you want to optimize the geometry subject to the constraint that the distance between the hydrogen atoms is 2 0 angstroms Then you would add the following coord section amp coord hi h2 2 0 amp 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 atom listed in the zmat section input Here is a sample connect section Jaguar 5 5 User Manual 167 Chapter 9 The Jaguar Input File amp connect Ch 2 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
365. n V H Ghuysen J M Theor Chim Acta 1992 82 189 Simons J Jorgensen P Taylor H Ozment J J Phys Chem 1983 87 2745 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 Jr Korsell K J Comput Chem 1982 3 385 Rabuck A D Scuseria G E J Chem Phys 1999 110 695 Jaguar 5 5 User Manual 327 References 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 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 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 Correction of Self Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen Bonding Effects J Phys Chem 1996 100 11775 Chasman D
366. n you can determine whether there is a lower or higher symmetry point 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 rota tion 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 4 Keyword isymm 8 in gen section of input file Jaguar 5 5 User Manual 37 Chapter 3 Running Jaguar From Maestro main Jaguar programs use a small tolerance 1 0 x 10 bohr which should result in molecular energy changes of 1 microHartree or less If you want you can turn the use of symmetry off in the Methods window For some calculations including GVB LMP2 GVB LMP2 and GVB RCI and those of IR intensi ties or hyperpolarizabilities symmetry is not yet implemented and is disabled automati cally 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 estab lishes what changes are acceptable In
367. n 10 3 2 on page 247 10 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 next line is made up of two integers The first integer dictates the number of dealiasing function sets provided for each atom type each set is used for a particular grid during 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 1 To see this connectivity information for a system set ip12 2 in the gen section 244 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files exceed 10 The sample file s second line indicates that for each ba
368. n 4 8 Lowercase or uppercase letters can be used Polarization and diffuse functions can be added by appending or immediately after the basis name The meaning of these symbols is also described in Section 4 8 If you use an atomic section to specify different basis sets for one or more atoms than the basis set used for the other atoms in the input you should not change any basis set assign ments if you later restart that job For instance if you run a job whose input file mixmol in contains an atomic section that specifies different basis sets for different atoms you can generate a new input file restart file called mixmol 01 in from the job but if you use this input file for a second job restarting the old calculation you may not change the atomic section at all otherwise the program misinterprets the initial guess specified in the guess section in mixmol 01 in Alternatively you can delete the guess section completely and then change the atomic section Three other keywords shown in Table 9 45 allow you to specify whether to include grid points dealiasing functions or nuclear charges for listed atoms The values n no none and only are not case sensitive You can use the atomic section to specify coun terpoise atoms and that settings in the atomic section take precedence over Z matrix Jaguar 5 5 User Manual 221 Chapter 9 The Jaguar Input File
369. n 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 69 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 Y 00653 00113 11356 16823 01169 04865 02 Z 07806 12275 08708 00749 00934 01566 03 X 07467 12140 11117 03829 00279 01163 03 Y 02320 01992 07655 17175 02320 01800 03 Z 03681 04285 05472 00584 13452 13276 F4 X 13055 00611 01869 00459 00502 00537 F4 Y 05236 09865 08436 00590 01826 01460 F4 Z 01586 04767 03106 01413 10532 10001 Thermochemical properties at 1 0000 atm 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 1430 30 1529 51 1563 02 Thermodynamic properties calculated assuming an ideal gas 122 Jaguar 5 5 User Manual Chapter 6 Output 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
370. n idft Where idft ijklm m in idft Local Exchange Functional or Exact Exchange m 0 exact exchange Hartree Fock m 1 Slater m 9 Xa Jaguar 5 5 User Manual 175 Chapter 9 The Jaguar Input File Table 9 11 Values of l in idft Where idft ijklm lin idft Non local Exchange Functional 1 0 none l 1 Becke 1988 nonlocal term only l 3 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 9 12 Values of k in idft Where idft ijklm k in idft Local 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 9 13 Values ofj in idft Where idft ijkIm jinidft Non local Correlation Functional j 0 none j 1 Perdew 1986 nonlocal gradient correction j 2 Lee Yang Parr local and nonlocal correlation j 3 HCTH407 nonlocal correlation functional j 4 Perdew Wang GGA II 1991 nonlocal correlation only j 6 Becke 1998 B98 nonlocal correlation functional j 7 Schmider and Becke 1998 SB98 nonlocal correlation functional j 8 B97 1 nonlocal correlation functional j 9 PBE nonlocal correlation functional 176 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table
371. n the load is lower could solve the problem Otherwise you might want to try an appropriate setting from Section 9 5 24 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 mem ory on your machine Contact us as described on page 319 if you would like any tips for setting memory use for your machine Jaguar 5 5 User Manual 287 Chapter 12 Troubleshooting 288 Jaguar 5 5 User Manual Chapter 13 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 workstations 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 references 136 and 137 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 Closed shell LMP2 single point calculations If you want to compute analytic frequencies you probably should run your Jaguar energy calculation or geometry optimization first in parallel then use the restart job for a frequency calculation in seri
372. nal combinations for SCF or post SCF DFT calculations 6 3 2 LMP2 If you perform a local MP2 calculation the output from the programs pre and hfig is somewhat 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 for these calculations and the symmetry labels are not included in the output of orbital energies 106 Jaguar 5 5 User Manual Chapter 6 Output The program loclmp2 which computes localized orbitals runs after scf in an LMP2 calculation 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 calcula tion 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 your choice from the LMP2 window of whether to use valence electrons only or all electrons for the atoms in the calculation Next the numbers of occupied and virtual orbitals for the molec
373. nally 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 userid This gives user userid rsh access to host bobcat schrodinger com Jaguar 5 5 User Manual 297 Chapter 13 Parallel Jaguar 13 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 automatically 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 into the of Processors window in the Jaguar Run panel By default the maximum number of proces sors 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 If you need to pass additional parameters to the POE or MPI launch commands you can set the environment variable SCHRODINGER POE FLAGS on IBM platforms or SCHRODINGER MPI FLAGS on all other platforms to the arguments that you want to pass in For example for verbose output from mpi run on an SGI set the following csh tesh setenv SCHRODINGER MPI FLAGS v sh ksh bash exp
374. name type NONE to return to ATOMIGFILE NONE default choice for that file type DAFFILE NONE GRIDFILE NONE CUTOFFFILE NONI GPTSFILE NONE WAVEFNFILE NONE xl remove a section RMSECTION section name RMSECTION guess RMSECTION gvb clear the gen section RESETGEN except for the multip and molchg settings 278 Jaguar 5 5 User Manual Chapter 11 Running Jobs Table 11 7 Definition of Options That Are Applied to a Template File to Generate an Input File Continued Change Format Examples insert a file at the top of ADDTOP filename ADDTOP guess in the input append a file to the input ADDEND filename ADDEND guess in substitute a value for a old pattern new pattern bond 1 5 variable Do not use any of the charac torang 170 0 ters lt gt in either pat tern 11 3 2 Batch Input File Example As an example 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 You can create a batch file that automates this process The batch file would read in each molecular geometry from an existing input file make the necessary keyword changes and perform the calculations Here is an example of such a batch file B3LYP 6 31G geometry optimization SJO
375. nched or when you choose Monitor from the Applications menu in the Maestro main window See Section 6 8 on page 136 for more information on this file Jaguar 5 5 User Manual 45 Chapter 3 Running Jaguar From Maestro The primary Jaguar output is contained in the output file which is created in the scratch directory of the host on which the calculation is run and is copied back to the local host when the job finishes The output file is described in Chapter 6 3 9 Other Maestro Features This section describes some features of Maestro that are not covered elsewhere Note that sometimes a menu item is dimmed which means that the option is currently unavailable For example the Run button is dimmed until a geometry is entered 3 9 1 Checking Jobs With the Monitor Panel The Monitor panel allows you to examine Jaguar log files It opens automatically when you start a job If you hide the Monitor panel you can reopen it again later by choosing Monitor from the Maestro Applications menu See Section 2 12 on page 19 and the Maestro User Manual for more information on job control and monitoring The log file for the last job you ran h20 10g for the job h2o for example is displayed automatically in the Monitor panel The log file indicates when each Jaguar program has finished running Section 6 8 on page 136 contains more information about this file 3 9 2 The Reset Option The Reset button in the Jobs section resets many of the settings
376. nd grid points not eliminated by cutoffs and the Fock matrix is assembled from its Coulomb and exchange matrix components J 5 and K ij which are calculated in physical space and transformed back into spectral space by the following equations dg Yel Y Au Du fs 3a g kl Ky od Y As Y Doha G 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 4 is given by Equation 2 The grid points used for each SCF iteration are 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 148 Jaguar 5 5 User Manual Chapter 8 Theory Jaguar actually uses the pseudospectral method described above for the majority of the computationally 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 GJIKDDy kl for cases in which i j k and meet certain cutoff criteria and the two electron integral ij kl is of the form aalaa aalab aalbb ablab or aalbc where a b and c indi cate the atom upon which the function is centered Sim
377. nding on which orbitals are printed 39 Relevant orbital output keyword set to 5 10 or 15 in gen section of input file depending on which orbitals are printed 40 Relevant orbital output keyword set to 6 11 or 16 in gen section of input file depending on which orbitals are printed 134 Jaguar 5 5 User Manual Chapter 6 Output 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 func tions 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 Because GVB orbitals are not computed until some time after the Hartree Fock initial guess you cannot choose to print GVB non orthogonal orbitals if you have selected after HF initial guess above Also note that in canonical orbital space the labels indicating atom identifiers and basis function types are meaningless If you generate output for occupied orbitals or all orbitals in the 19 15 or f8 5 formats you can use it for input in the guess section of an input file which is described in greater detail in Section
378. 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 problems 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 specify the display with the following command substituting the name of your X server or terminal for displayhost csh tcsh 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
379. nput file Jaguar 5 5 User Manual 55 Chapter 4 Options slider marked Pair set at 1 Next specify the atom numbers for the atoms in that pair using the Atom 1 and Atom 2 sliders or by clicking in the slider box The appropriate atom labels for example H2 are displayed to the right of the Atom 1 and Atom 2 boxes and reflect the atoms selected in those boxes Additional pairs can be entered in the same manner after specifying a new pair number with the Pair slide bar You can also combine the user input pairs and heteroatom pairs options setting your own LMP2 pairs in addition to all heteroatom pairs 4 3 Generalized Valence Bond GVB Settings The window opened when you click GVB allows you to request a generalized valence bond GVB calculation and to set the GVB pairs for that calculation You can also choose to do a restricted configuration interaction RCI calculation 12 48 49 for some or all of the pairs The theory behind GVB and GVB RCI calculations is explained in Chapter 8 The default Jaguar calculation is closed shell or open shell Hartree Fock depending upon the number of electrons in the system To include electron correlation with the General ized Valence Bond Perfect Pairing GVB PP method 20 you can provide a list of GVB pairs to be used in the calculation Specifying this list automatically enables GVB The GVB and GVB RCI methods in Jaguar do not include the concept of resonance Consequently the GVB or GVB
380. ns 0 0 eects 121 geometry and transition state OptiMIZAtiONS eee 109 GVB calculations 107 GVB RCI calculations 108 GVB RCI optimizations 112 LMP2 calculation options 106 properties i n stb entree 116 solvation calculations 112 output options oo ee eects 106 136 atomic units eee aesti 125 bond lengths and angles 125 connectivity table 125 detailed timing information 125 echo input file and parameter list 124 files aunt 129 131 206 339 Index Gaussian function list basis set 126 Gaussian function list derivatives 129 geometry optimization details 126 memory disk and i o information 124 one electron Hamiltonian 126 orbitals 133 136 208 210 overlap matrix eeeeeee 126 per iteration 131 132 207 208 standard 124 129 204 205 output summarizing eee 97 102 output see output file output options standard output file output options per iteration out put options orbitals babel overlap matrix in DIIS error vector 105 137 keyword for eigenvector and eigenvalue QUEDUE ariarian iiA 205 keyword for output of 205 output option eene 1
381. ns in the block choose Undo from the Edit menu Undo is not supported for all Maestro operations An undo block will be created only if at least one undoable operation has been performed since the Begin Undo Block command was issued 2 10 Maestro Command Scripts Although there is a provision for performing nearly all Maestro supported operations through menus and panels the operations can also be performed using Maestro commands or compilations of these commands called scripts Jaguar 5 5 User Manual 17 Chapter 2 The Maestro Graphical User Interface Command Script Editor script Command History The Command History window displays a log of Select All Deselect All Show Hide Opens the Show all Maestro com ji TEST ni ea iiid mands issued panel which dis W Log Commands internally when plays commands you interact with Script logged in the a panel menu ORIESSSHEE Command History or structure projectopen zone1 juliem test projects QuickTopics prj list hidepanel table showpanel import entryimport format any entryimport format maestro hidepanel import showpanel script va Run Script i Expand Command Aliases Open Local Open Global Save As Hide Help Figure 2 5 The Command Script Editor panel Command scripts can be used to automate lengthy procedures or repetitive tasks Because all Maestro commands are logged and displayed in the Command Script Editor panel
382. nstance 6 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 6 3 on page 106 describes the variations in the output file for the calculation options described in Chapter 4 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 individual Jaguar program run for a default calculation The output from the program pre begins with a description of the calculation to be performed its job name the directory containing the executables used to run the job the directory containing the temporary files comments from the input file if any and the names and paths of any non default data files used for the calculation as explained in Section 9 1 on page 161 and Chapter 10 Comments from the input file include any text entered in the Comment box in the Run or Save window as well as a comment about the point group if the geometry was symmetrized as described in Section 3 5 2 on page 37 Next the basis set used for the calculation the molecule s net charge and multiplicity and the number of basis functions used for the ca
383. ntain the pair settings in any order unless you are using the Lewis dot structure keywords described in Section 9 5 5 on page 170 Each line describing a bond pair should contain three integers which specify the type of bond 1 for sigma 2 for pi 3 for a 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 identi fying 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 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 respectively 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 0 entry is a place holder and a 1 entry indi cates 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 indicate the CI coefficients for the first and second GVB natural or
384. nter over the element If there is Bal loon help for the element it appears within a few seconds If you do not find the help you need using the steps above click the Help button in the lower right corner of the panel for whose settings you are seeking help The Help panel is displayed with a relevant help topic For help with a concept or action not associated with a panel open the Help panel from the Help menu or use the key combination ALT H Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface If you do not find the information you need in the Maestro help system check the following sources The Maestro User Manual The Maestro Release Notes The Frequently Asked Questions page found at http www schrodinger com Support faq html If you do not to find answers to your questions in any of these places contact Schr dinger using the information below Schr dinger E mail help schrodinger com USPS 1500 SW First Ave Suite 1180 Portland OR 97201 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com Generally e mail correspondence is best because you can send machine output if neces sary When sending e mail messages please include the following information most of which can be obtained by entering SCHRODINGER machid at a command prompt Purchaser of the software Primary user of the software Platform type Jaguar vers
385. ntly selected and allow you to make functional choices not available from the DFT Model options described above If you make a choice from these menus that does not correspond to a DFT Model option the DFT Model option changes to Custom The Hybridization menu choices are Half amp Half and Becke 3 par If you choose one of these the Hartree Fock treatment of the exchange and the contributions of the functional terms selected are weighted by coefficients from either Becke s Half amp Half method or his three parameter method The Exchange menu choices include two local exchange functionals Slater and Xo 29 and two combinations of local and nonlocal functionals combining Slater local exchange with either the Becke 1988 32 or the Perdew Wang 1991 GGA II 31 non local exchange correction term If you do not make a selection Jaguar uses the exact Hartree Fock exchange However if you are using a hybrid method you should select an exchange functional from the menu The local correlation functional options are two functionals by Vosko Wilk and Nusair 30 labeled VWN and VWN5 Perdew and Zunger s 1981 functional 34 labeled PZ81 and Perdew and Wang s 1991 local correlation functional 31 labeled PW91 Nonlocal correlation options are Perdew s 1986 gradient correction functional 35 labeled PW86 Perdew and Wang s 1991 generalized gradient approximation correlation functional 31 labeled GGA II and the Lee Yang Parr functi
386. nual Chapter 14 The pK Prediction Module 14 1 Introduction Schr dinger s pK prediction module represents the first attempt to utilize ab initio quantum chemical methods to reliably predict pK values in aqueous media 144 The module employs a combination of correlated ab initio quantum chemistry a self consis tent reaction field SCRF 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 trac table computational requirements The user interface to the methodology 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 ioniz able groups relevant to the chemical and pharmaceutical industries are specifically designed to work with the basis sets electron correlation levels and solvation model of the ab initio methodology The transferability of the corrections has been tested by exam ining 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 qu
387. ny user specified subset of the GVB pairs A GVB mean field procedure is then used to evaluate a Coulomb exchange mean field operator describing the effect of the non excited GVB pairs on the RCI pairs This treat ment 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 configu ration s calculation The RCI spatial states S 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 TE M Eb Jw uujvy eoue c vwa Le Ypg vu Ks uv py awol kowo VE Wig Yad Fiz 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 J oB y8 ay O Be Ype Vp Y 9e Wag Vg gt Kgs ay B9 154 Jaguar 5 5 User Manual Chapter 8 Theory 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 6 natural orbitals are from the same RCI pair with index q The complicated part of the calculation of the Coulomb and exchange opera tors then is evaluating matrix elements in atomic orbital
388. o be careful about using these names for new files The rest of 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 Jaguar 10 1 The Basis Set File The basis sets available for use in Jaguar appear in the file default basis in the stan dard 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 10 1 1 Format of the Basis Set File The basis sets are described in turn Basis sets at the top of the file do not contain effective core potentials and will be described first here The basis sets with effective core poten tials whose names begin with LA will be described later 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 4 3 on page 71 or Table 4 4 on page 73 and any other names which describe the same basis set e g STO 3G and STO3G The basis set names are separated by commas and must Jaguar 5 5 User Manual 237 Chapter 10 Other Jaguar Files include and or characters if those are allowed for that b
389. o use a converged HF wavefunction as the basis for the GVB initial guess For this option select compute from HF converged wavefunction for the GVB initial guess setting and make the appropriate setting under HF initial guess for the 69 Keyword iguess 10 in gen section of input file 70 Keyword iguess 25 in gen section of input file 71 Keyword iguess 30 in gen section of input file 72 Keyword iguess 1 in gen section of input file 73 Keyword ihfgvb 2 in gen section of input file or keyword ihfgvb 0 if iguess is not 1 74 Keyword ihfgvb 1 in gen section of input file 76 Jaguar 5 5 User Manual Chapter 4 Options Hartree Fock calculation Because this selection requires two SCF calculations one for HF and one for GVB it is considerably more expensive than using the GVB initial guess 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 wavefunction from the input file s guess section and to use that as the initial guess for the calculation For instance if you were restarting a job as described in Section 7 2 on page 142 and wanted to use the result from the previous run as an initial guess for the new run the Read from input option for the GVB initial guess would allow you to do so 4 9 4 Convergence Issues We recommend using the default Direct Inversion in the Iterative Subspace DIIS or GVB DIIS SCF converg
390. ollowing ways e Select the nodes using the HOST option of the jaguar run command The list of nodes must be enclosed in quotes e Create a local machines LINUX file listing the nodes you want to use and set the environment 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 13 1 2 5 Troubleshooting Parallel Job Problems If the jobname 10g 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 trans ports the environment variables including SCHRODINGER to all job nodes If serv p4 is not running or if it is using the wrong communication port which must match your MPI PASSPORT value or if MPI_USEP4SSPORT is not set or is misspelled then SCHRODINGER is not set correctly and this error message results If the jobname 1og file contains the error message p4 error OOPS semop lo
391. on Other Nodes 285 12 2 Other Problems eia ease ione eret olet diat EE ES 286 Chapter 13 Parallel Jaguar eee eee eee cesses ette eene en stantes sensns tn sena 289 13 1 Installing Parallel Jaguat ceret et tnt 289 13 1 1 SGI Installation rrr tte ere trente repone 290 13 1 2 LINUX Installation rrr rentre 291 3 1 2 1 Installing MPICH ette ttt hereto etn tiere 291 13 1 2 2 Comme uration sci 13 inis aassiacleteeincielscateieaiaasccniaaeais 291 13 1 2 3 Launching the Secure Servers eee 293 13 1 2 4 Selecting Nodes fora Job eee 295 13 1 2 5 Troubleshooting Parallel Job Problems 295 131 3 IBM Installation rti eti e cerei rre ertet t a 296 13 2 Rimning Jobs m Parallel sao reine eerte ete eaaet etre chev sees ar erie 298 Jaguar 5 5 User Manual ix Contents Chapter 14 The pKa Prediction Module ceeeeeeeeeeeeerene 299 T4 1 Introduction see eet te rrt ente en rete aenea E beate tpe ieee 299 14 2 Theory of pKa Calculation eene ir tr ertet niai iaia i aaRS 300 14 2 1 Ab initio Quantum Chemical Calculation of pKa Values 300 14 2 2 Empirical Corrections 3 secedsecdeccivscsesveseatedaacesceeeitecnasege scoieeseavevias 302 14 3 Predicting pKa Values in Complex Systems sese 303 14 3 1 Conformational Flexibility eee eee rete 303 I ao Bs lionis
392. on 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 Hamiltonian 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 information in the SCF output for a water mole cule with two GVB sigma pairs Jaguar 5 5 User Manual 107 Chapter 6 Output Total Coulomb Exchange Total two electron terms 37 90378136033 46 96140169504 9 05762033471 Hamiltonian 1 25 77166631229 32 84704880440 7 07538249211 Hamiltonian 2 6 02807668738 6 99023521309 0 96215852571 Hamiltonian 3 6 02990515066 6 99271668375 0 96281153309 Hamiltonian 4 0 03711925295 0 06576591758 0 02864666463 Hamiltonian 5 0 03701395705 0 06563507622 0 02862111917 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 ee 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 SCFE SCF energy GVB 76 06328826029 hartrees iterations
393. on dialog box to select the atoms or open the Atom Labels panel with the Composition tab displayed to select the composition of the label The picking choice is persistent Double clicking applies the label to all atoms Measure distances angles or dihe drals Displays a menu from which you can choose between distance angle or dihe dral The choice is persistent The default is distance After clicking this sistent button pick atoms in the workspace to define the measurement 2 7 Mouse Functions The mouse functions common to graphical user interfaces are supported in Maestro The left button is used for selecting choosing menu items clicking buttons and selecting objects This button is also used for resizing and moving panels Other common mouse functions such as combinations with the SHIFT or CTRL keys are used in some contexts for selecting a range of items and selecting or deselecting a single item without affecting other items 2 7 Mouse Functions in the Workspace The Workspace has special uses for the middle and right mouse buttons These are used alone and in combination with the SHIFT and CTRL keys to perform common operations such as rotation translation centering and zooming Apart from centering a molecule on an atom all these operations involve dragging If you have the handedness on your mouse set to left the mouse functions are the mirror image of those described the right mouse button is used for
394. onal 33 which includes both local and non local terms labeled LYP L NL As an example to set up a calculation using Becke s three parameter method to weight the Slater Becke 88 exchange functional Perdew and Zunger s 1981 local correlation func tional and Perdew s 1986 non local gradient correction functional you could select Becke 3 par from the Hybridization menu Slater Becke 88 from the Exchange menu PZ81 from 22 Keyword dftname b98 in gen section of input file 23 Keyword dftname sb98 in gen section of input file 24 DFT keyword settings are extensive and complicated so further options are not footnoted See Section 9 5 7 on page 173 for more information Jaguar 5 5 User Manual 53 Chapter 4 Options the Local Correlation menu and Perdew 86 from the Non local Corr menu As another example you could select the Half amp Half option from the DFT Model choices then add functionals by selecting for instance Slater Becke 88 to add Becke s non local gradient correction to the exchange functional and LYP L NL for a correlation treatment 4 2 Local MP2 Settings The Local MP2 button opens a window that allows you to set up a local M ller Plesset second order perturbation theory 42 45 calculation The local MP2 LMP2 method greatly reduces the basis set superposition errors that can arise from the canonical MP2 method 45 The LMP2 method is much faster than canonical MP2 and typically recovers 98 of th
395. ond method see GVB calculations geometry input oe eee 26 35 Cartesian format 27 28 29 164 editing deett 26 28 file types for scanning 34 35 FOPMA tiair 164 168 input file sections for 164 168 key WOtdS cscncocacac etre ete 168 output file echoed in 102 sample calculation 24 symmetrizing eee 37 38 286 troubleshooting sse 286 units input keyword 165 units keyword for 164 168 229 Z matrix format 27 29 32 164 166 geometry optimization 83 94 calculating forces only 83 180 constraining bond lengths or angles 32 86 87 166 181 constraining Cartesian coordinates 29 86 87 convergence criteria 84 84 85 111 183 detailed output option for 126 frozen bond lengths or angles for 32 86 87 166 181 frozen Cartesian coordinates for 29 86 87 GDIIS method sss 181 generating input with new geometry 141 in solution 58 60 180 188 initial Hessian for 32 33 85 93 165 181 182 input file section for Hessian 226 227 keywords for sss 179 183 limiting step size for 85 86 183 184 188 maximum number of iterations
396. one electron Hamiltonian keyword for output of 205 output option eeeeennn 126 one electron integrals 102 energy contributions 113 115 131 open shell singlet keyword for 199 open shell systems eene 74 energy contributions in output 105 keywords for sssrini 194 Optimization window 83 94 optimizing geometry eee 83 94 calculating forces only 83 180 constraining bond lengths or angles 32 86 87 166 181 constraining Cartesian coordinates 29 86 87 convergence criteria 84 85 111 183 convergence criterion for SCF 84 detailed output option 126 fixed bond lengths or angles TOF seio deed 32 166 181 fixed Cartesian coordinates for 29 frozen bond lengths or angles for 86 87 frozen Cartesian coordinates for 86 87 GDIIS method keyword 181 generating input with new geometry 141 in solution esssess 58 60 180 initial Hessian for 32 33 85 93 165 181 182 226 227 keywords for sss 179 183 limiting step size for 85 86 183 184 188 maximum iterations 83 141 181 Gutput from nn ai enitn 110 output of forces 109 output options oo eects 125 refinement of in
397. onic solvation fitting to this data does not lead to the large uncertainties that would be associated with the ionic solva tion data Additionally there is an exceptionally large database of known pK values for a wide range of chemical functional groups Jaguar 5 5 User Manual 301 Chapter 14 The pKa Prediction Module In general the dielectric radii of ions particularly negative ions are expected to be smaller than that for the corresponding neutral species due to the phenomenon of electros triction 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 14 1 on page 306 For novel functional groups with divergent electronic properties reparameter ization 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 substit uent and conformational effects once a functional group is parameterized In our work on neutral solvation we have found that it is necessary to supplement param eterization of dielectric radii with surface area terms to correct for fir
398. ons as they are when you use the babel and babelg keywords in a Jaguar input file The input and output file names given 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 structure 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 number 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 274 Jaguar 5 5 User Manual Chapter 11 Running Jobs write individual Jaguar input files Cartesian for the 5th through 10th intermediate struc tures in a Jaguar geometry optimization run type the command jaguar babel ijagout job out 5 10 ojagc iter in split The files iter0
399. ons from the beginning of the first SCF calculation in a run are considered to be part of the preliminary 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 wavefunction are preliminary iterations followed by final itera tions 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 updating iterations in the final sequence respectively Finally the last column dictates the cutoff sets used for non SCF calculations as for gradient calculations 252 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files The first six lines of the default cutoff file which illustrate these points are cutv0300 1 r1 77 ma
400. ontains information on running calculations on parallel computers Chapter 14 describes the pKa calculation module 1 1 Conventions Used in This Manual In addition to the normal use of italics for names of documents the font conventions that are used in this manual are summarized in Table 1 1 Table 1 1 Font Conventions Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons labels Monospace SSCHRODINGER maestro File names directory names commands and environment variables Italics filename Text that the user must replace with a value Sans serif ALT H Keyboard keys uppercase Bold atomic Input keywords Bold italic 0 Default value of a keyword Used in tables of keyword values In descriptions of command syntax the usual UNIX conventions are used braces enclose a choice of required items square brackets enclose optional items and the pipe symbol separates items in a list from which one item must be chosen References to literature sources are given in square brackets like this 13 The reference list begins on page 321 2 Jaguar 5 5 User Manual Chapter 1 Introduction Superscripts in the text correspond to footnotes that list the Jaguar input file entries that correspond to particular GUI settings You can ignore the footnotes if you like but you may find them useful for setting up files to run calculations without using the GUI or for in
401. opriate option The buttons are described below Open a project Import structure s Displays the Open Project dialog box T E Displays the Import panel Show Hide Project Table Create entry from Workspace Displays the Project Table panel or EH Ed Creates an entry in the current project hides it if it is displayed using the contents of the Workspace Show Hide Build panel Delete Displays the Build panel or hides it if it ya x Displays a three section menu from is displayed i which you can choose an object to delete The first section is a pick menu for deleting atoms by picking If you select one of these items the delete but ton is indented to show that you are picking to delete atoms The pick state is persistent The second section opens the Atom Selection dialog box to define atoms to delete The third section allows you to delete other objects associated with the structures in the Workspace Local transformation i Undo Redo Displays a menu from which you can rS Undoes or redoes the last action Per select the object for local transforma a forms the same function as the Undo tion or open the Advanced Transfor item on the Edit menu and changes to mation panel The selection is an arrow pointing in the opposite direc persistent tion when an Undo has been performed indicating that its next action is Redo Fit to screen Clear Workspace T RA m Scales what is displayed so it fits into ET rr Y the Workspace Set
402. ord for output of 205 quadratic synchronous transit see QST guided transition state searches quitting Maestro esee 25 R radian units for geometry input 168 radius Covalent iic Dre ete 221 van der Waals eese 221 Jaguar 5 5 User Manual Index RCI restricted configuration interaction calculations 56 57 153 155 216 output from ee 107 108 109 CX PLOSLAM errer na a 232 reactant geometry for IRC calculations 95 in transition state search 89 specifying in input file 165 specifying in Maestro 90 Read window esee 34 35 reading input files sss 34 35 filetypes iei 34 35 286 geometry input eeeeee 34 35 troubleshooting esses 286 reset option Jaguar panel 46 RESP file Key Word fot nie te 207 restarting calculations Initial SU688 oiii 76 restart file essssssssss 206 207 with improved guess 141 Restarting jobs see 142 restricted configuration interaction see RCI calculations restricted open shell wave functions keyword for seeeeese 194 OPtiOn fOE a eec a 74 results summary of eese 97 102 lire
403. ord 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 9 1 on page 161 The ip172 2 setting instructs Jaguar to write out a file named jobname resp containing the electrostatic potential data see the text under Table 9 32 Table 9 24 Real valued Property Keywords Keyword Default Value Description cfiterr 1 0 x 10 Allowed error in electrostatic potential charge fitting when fitting is constrained to reproduce multipole moments wispc 0 75 Spacing in bohr of rectangular grid for ESP fitting denspc 0 75 Spacing in bohr of rectangular grid for electron density cal culation efield 0 024 Electric field for polarizability and hyperpolarizability cal culations in au default is 0 006 for ipolar 1 9 5 13 Frequency Related Keywords For jobs that include a calculation of vibrational frequencies various frequency related properties can also be computed by setting the appropriate keywords Most of these keywords which are listed in Table 9 25 correspond to GUI options described in Section 4 7 on page 64 Only the values listed in the table are allowed The thermochemical properties are listed in cal mol K and kcal mol by default Use the output option ip28 2 for output in J mol K and kJ mol When the calculation of vib
404. ords default values generally depend on other keywords By default Jaguar calcu lations are performed in the gas phase so isolv 0 and all other solvation keywords are irrelevant Table 9 21 Integer Keywords for Solvation Calculations Keyword Value Description isolv 0 Do not perform a solvation calculation 2 Perform a solvation calculation using Jaguar s Poisson Boltz mann solver 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 key word ivanset 1 by default ivanset 0 Do not set van der Waals radii according to Lewis dot structure 1 Set van der Waals radii according to Lewis dot structure lewstr 1st structure by default see Section 9 5 5 on page 170 and Section 10 6 on page 253 kesep 0 Combine terms for all one electron matrices 1 Keep kinetic energy terms nuclear attraction integrals and point charge terms separate Note if isolv 1 or 2 kesep 1 by default isolvg 0 Compute gradients in solvation with method used for Jaguar ver sion 3 5 and earlier 1 Compute gradients in solvation with more robust method for version 4 0 on Jaguar 5 5 User Manual 187 Chapter
405. ort 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 When you are choosing the number of processors to use for a parallel Jaguar job divide the number of basis functions for the job by 100 for HF or DFT jobs or 80 for LMP2 jobs then discard any portion of this number after the decimal place This number is the maximum number of processors advised for an efficient parallel run For instance if your molecule had 486 basis functions the maximum number of processors advised for an HF or DFT calculation is 4 and the maximum number of processors for an LMP2 job is 6 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 j exec always runs as a separate process Jaguar batch jobs cannot use MPI for the individual subjobs If you request multiple processors for a batch job with multiple input structures or files the subjobs are distributed over the available processors with one job per processor 298 Jaguar 5 5 User Ma
406. ot calculation settings The output can be generated at the end of each iteration in a geometry optimiza tion 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 9 30 Table 9 30 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 Batchmin command file box DOCK 3 5 box file caccrt Cacao Cartesian file cacint Cacao Internal file cache CAChe MolStruct file c3dl Chem3D Cartesian 1 file c3d2 Chem3D Cartesian 2 file cdet ChemDraw Conn Table file Jaguar 5 5 User Manual 201 Chapter 9 The Jaguar Input File Table 9 30 Output Format Keywords and File Types for Babel File Format Conversions Cont d Format Keyword File Type 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 sdf MDL Isis SDF file jagz Jaguar Z Matrix file jage Jaguar Cartesian file m3d M3D file macmol Mac Molecule file macmod Macromodel file micro Micro World fil
407. ource code is always available from http www unix mcs anl gov mpi mpich Instructions for building and installing MPICH are included with the source code When you build MPICH from the source code include the following configure options with comm shared with device ch p4 The directory in which you installed MPICH is referred to below as MPICH install 13 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 Edit the file MPICH_install share machines LINUX and list the names of the hosts available for parallel calculations Each line of this file should specify the name of a host and the number of processors on that host separated by a colon The host name should match the output of the hostname command For example homer mynet edu 2 marge mynet edu 2 bart mynet edu 1 Jaguar 5 5 User Manual 291 Chapter 13 Parallel Jaguar 3 Edit the schrodinger hosts file in the directory where Jaguar was installed and list in it the names of the hosts in the machines LINUX file The host names in schrodinger hosts need not include the domain name See Section 11 1 on page 263 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 Schrod
408. ourth and fifth basis functions are generated in the same way as the third but with different polynomials 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 function 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 normaliza tion constant for the primitive Gaussian shell N is listed in the column labeled rcoef Gaussian Functions Shell information S j h c i n e o S f 1 n h S atom 1 Eus d h Zz coef rcoef Oo 1 6 0 1 0 5484 6716600 0 0018311 0 8317237 Oo 2 1 0 1 0 825 2349460 0 0139502 1 5308156 Oo 3 1 0 1 0 188 0469580 0 0684451 2 4771485 O 4 1 0 1 0 52 9645000 0 2327143 3 2562811 O 5 1 0 1 0 16 8975704 0 4701929 2 7928934 O 6 1 0 1 0 5 7996353 0 3585209 0 9549377 O 7 3 d cu 1 15 5396162 0 1107775 0 6179340 Oo 8 7 3 1 1 3 5999336 0 1480263 0 2757209 Oo 9 7 3 1 1 1 0137618 1 1307670 0 8142076 O 10 3 1 2 2 15 5396162 0 0708743 3 1169443 Jaguar 5 5 User Manual 127 Chapter 6 Output Oo 1I E0 14 2 2 3 5999336 0 3397528 2 4014375 Oo D2 10 21 2 2 1 0137618 0 7271586 1 0543604 Oo 13 tAr cd 5 0 2700058 1 0000000 0 2669562 Oo 14 1 1 2 6 0 2700058 1 0000000 0 2774320 Oo 15 L1 0 3 9 0 8000000 1 0000000 1 1138249 H1 1 3B lt 2 15 18 7311370 0 0334946 0 214
409. owed by arguments on the same line sections describing the molecule and the calculation whose formats will be described later in this chapter or comments The input file should have the following format where symbols 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 grid CUTOFFFILE file path name cutoff LEWISFILE file path name lewis GPTSFILE file path name The last six lines are only rarely used Therefore generally your Jaguar input files will take a form as simple as sections describing molecule amp calculation where only the zmat section which contains the geometry and will be described later in this chapter is actually required Jaguar 5 5 User Manual 161 Chapter 9 The Jaguar Input File The basis atomig initial guess information daf dealiasing functions grid cutoff and lewis data files are described in Chapter 10 If you want to use non default choices for any of these files you can specify their paths and names on the appro priate lines of the input file If a file name listed in the input file 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 anoth
410. oy 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 localization see text in this subsection 200 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File When the keyword ixtrboy described in Table 9 29 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 orbitals for multiple bonds may therefore be diagonalized using the one electron Hamiltonians The output for this proce dure 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 significant Mulliken populations on the same pair of atoms is diago nalized 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 9 5 18 File Format Conversion Keywords You can call the program Babel 24 from Jaguar to generate files in any of a variety of formats although the files produced by Babel contain only geometries n
411. p12 2 in gen section of input file Sy Suc Jaguar 5 5 User Manual 125 Chapter 6 Output 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 9 5 1 on page 168 If a connectivity table entry is 2 the corresponding row and column atoms are each bonded to some same third atom by the definition 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 the geometry optimization details option is selected much 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 t
412. pace due to being lowest in energy in their respective class This is probably a reasonable assumption for many problems Note Jaguar 5 5 User Manual 303 Chapter 14 The pKa Prediction Module that the conformation that is lowest in the protonated state may not be lowest in the deprotonated state In many cases there are obvious electrostatic reasons why a con formational change upon protonation or deprotonation would occur The program is set up to accept a different conformation for each species The selection of the appropriate conformation can be nontrivial Our recommenda tion 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 pro cedure 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 Preliminary results indicate that there are situations where a solution phase conformational search is necessary to obtain accurate results 2 A more accurate approach is to 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 pro tonation state and compute the pK from this value This method i
413. peci fied host If no host is specified the local host is used If version args is ALL list all available versions of Jaguar even if not compatible with the specified host HOSTS List the hosts that are available for Jaguar calculations ENTRY Show the section of the schrodinger hosts file that will be used for this job WHY version args Gives information about why the specified version was selected Table 11 3 Version Options Option Description REL version Release version number v42 v4 2 42 v42062 41059 v4 1 049 are all acceptable forms VER pattern Pattern to match in the path to the executable Replaces v ARCH platform Platform code e g Linux IRIX mips4 268 Jaguar 5 5 User Manual Chapter 11 Running Jobs 11 2 1 Selecting a Calculation 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 11 1 on page 263 for a description of the schrodinger hosts file 11 2 2 Selecting Particular Jaguar Executables By default Jaguar looks for
414. picking and the left button is used for translating If you have a two button mouse make sure that it is configured for three button mouse simulation Then the middle mouse button is simulated by pressing or holding down both buttons 14 Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface Table 2 1 Mapping of Workspace Operations to Mouse Buttons and Keyboard Keys Operation Keyboard Mouse Combination Rotation about the x or y axis Rotation about the x axis only Rotation about the y axis only Rotation about the z axis Spot centering on an atom Translation in the x y plane Translation along the y axis Translation along the x axis Translation about the z axis Middle mouse button SHIFT and middle mouse button with vertical movement SHIFT and middle mouse button with horizontal movement CONTROL and middle mouse button with horizontal move ment Right click Right mouse button SHIFT and right mouse button with vertical movement SHIFT and right mouse button with horizontal movement CONTROL and right mouse button with horizontal movement Zoom Middle and right mouse buttons or SHIFT CONTROL and middle mouse button with horizontal movement 2 7 2 Mouse Functions in the Project Facility The standard combinations of SHIFT and CTRL keys with a click to select objects are supported in the Project Table To select a range of entries click the first entry hold down the SHIFT key and click t
415. pin Sz lt Sz 1 gt SCF post SCF method Energy related Options energy enuc egas esoln esolv esolute esolvent ereorg homo 98 final molecular energy nuclear repulsion energy gas phase energy solution phase energy solvation energy solute energy solvent energy solvent reorganization energy HOMO energies Jaguar 5 5 User Manual Chapter 6 Output Table 6 1 Options for the jaguar results Command Continued Option Meaning lumo LUMO energies gap HOMO LUMQO 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 208 15 K cv heat capacity Cv at 298 15 K int_energy Utot Htot Gtot pka pkb dipole internal energy U at 298 15 K Total internal energy Utot at 298 15 K including the SCF energy and zero point energy Total enthalpy Htot at 298 15 K including the SCF energy and zero point energy Total Gibbs free energy Gtot at 298 15 K including the SCF energy and zero point energy pKa pKb total dipole moment Geometry Optimization Options iterg stepg zvar name grms gmax drms dmax echange Timing Options time tscf trwr Jaguar 5 5 User Manual geopt iteration number geopt step number z variable value must be followed by zvar name rms gradient maximum gradient component rms displacement maximum displacement energy change total c
416. points using the text boxes at the bottom of the Calculate Surfaces window After you make your selection click RUN Jaguar launches a job to generate the plot data and the Monitor panel is displayed When the job finishes the surfaces are imported into Maestro and the first surface is displayed If your molecule is not already an entry in the Project Table the surfaces are not automatically incorporated To display the surfaces select the entry in the Project Table for the chosen molecule choose Surfaces from the Applications menu and then choose Import Surface Volume from the Surfaces menu 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 Job Host localhost Parir B 2a Electron density Spi density Electrostatic Potential Molecular Orbitals energy 359681 j Elu Ap symme energy 307174 A2u syne energy 288573 E2g Ap symme energy 288573 E2g App sym energy 209134 E1g Ap symme eta i of f Box length adjustment Ang fp 000 Grid density pts Ang 14 720 RUN Don t Run Help Figure 4 10 The Calculate Surfaces window 80 Jaguar 5 5 User Manual Chapter 4 Options side by side you must duplicate the Project Table entry for the molecule as many times as you have orbitals to view then create a separate orbita
417. port the DEL keylist which means that Natural Energy Decomposition Analysis NEDA is not supported The DELH keylist is also not supported The generation of plot data is incompatible with NBO calculations 236 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files Jaguar needs certain 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 functions 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 lewis 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 directory 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 9 1 on page 161 for more details If you specify a cutoff file called accurate cutoff quick cutoff or solvent cutoff the program assumes you are using an outdated file and will reset the name to default cutoff s
418. prepared as an initial guess for a transition state search 3 5 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 accurate enough for the desired symmetry to be recognized You can symmetrize the molecule using the Symmetrize Molecule button in the Geometry Cleanup window The point group symmetry that is used is displayed at the top of the window and is determined by Jaguar 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 rota tions and inversions are applied to determine the point group of the molecule 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 by default This value ensures that the highest symmetry is found in most cases By changing the value and clicking the Find Symmetry butto
419. pu time for job total time in scf cumulative total time in rwr cumulative 99 Chapter 6 Output Table 6 1 Options for the jaguar results Command Continued Option Meaning 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 6 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 where the first line lists the final 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 infor mation listed The columns appea
420. put file obtained by SCF calculations on atoms note that if guess section exists this is not the default choice 11 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 198 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 28 Initial Guess Keywords Cont d Keyword Value Description 25 For a system that contains transition metal atoms construct a high quality initial guess using ligand field theory as described in reference 19 Not available for GVB calculations 30 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 reference 19 Not available for GVB calculations ihfgvb 0 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 is not 1 1 Converge HF wavefunction where the initial guess is deter mined by iguess and use converged HF wavefunction as input to program gvbig to get GVB initial guess 2 Calculate a GVB initial guess from HF initial guess whose ori gin is determined by setting iguess ihamtyp 0 Construct Hamiltonian using standard core open and GVB orbitals 2 Make highe
421. r 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 atoms are X or Du An example of the use of a dummy atom for CH4OH input follows C O C 1 421 H1 C 1 094 Oo 107 2 X1 e 1 000 Oo 129 9 H1 180 0 H2 1 094 X1 54 25 H1 90 0 H3 C 1 094 X1 54 25 H1 90 0 H4 Oo 0 963 C 108 0 H1 180 0 Jaguar 5 5 User Manual 31 Chapter 3 Running Jaguar From Maestro 3 2 7 Constraining Z Matrix Bond Lengths or Angles To freeze bond lengths or angles during a geometry optimization add a sign after the coordinate values For example to fix the HOH bond angle of water to be 106 0 you could type 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 5 2 on page 86 which describes how to set up constraints for optimizations To constrain two quantities to be the same during a geometry optimization use variables in Z matrix input see Section 3 2 6 on page 31 To freeze variables during an optimiza tion 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 1 094 HCHang 109 47 You should not make any constraint changes from the Edit Geometry window or
422. r 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 4 3 on page 71 and Table 4 4 on page 73 including the char acters indicating 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 corresponding number 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 The second line for the same atom type should list real dealiasing exponents for each uncontracted 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 expo nent would be N re 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 wit
423. r in the table in the same order they are listed in the jaguar results command For instance the command 100 Jaguar 5 5 User Manual Chapter 6 Output jaguar results title jobname method energy h20 0ut h20 b3lyp out where h20 out and h2o0_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 h2o HF 76 023641 h2o0_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 infor mation 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 6 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 information from each geometry SCF or gradient calculation be reported in a different row of the results table For instance the command jaguar results titl
424. r 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 Energy Decomposition Analysis calculations from Jaguar however See Section 9 18 on page 236 and the NBO Program Manual for more details on NBO input and output 4 7 Frequencies and Related Properties Using the Frequencies window you can request calculations of frequencies infrared IR intensities and thermochemical properties heat capacity entropy enthalpy and Gibbs free energy Vibrational frequencies and thermochemical properties can be computed for HF DFT LMP2 or GVB wavefunctions except that numerical frequencies cannot be computed for unrestricted HF or DFT wavefunctions IR intensities are computed by default for frequency jobs for which either a analytic HF frequencies are computed and the basis set does not have any effective core potentials see Section 4 8 on page 70 for details or b HE GVB or DFT frequencies are computed numerically The results of frequency calculations can be animated in Maestro 47 Keyword mulken 1 in gen section of input file 48 Keyword mulken 2 in gen section of input file 49 Keyword mulken 3 in gen section of input file 50 Empty nbo section in input file amp nbo amp 64 Jaguar 5 5 User Manual Chapter 4 Options Frequencies Vibrational Frequencies Atomic masses Pulay SQM
425. r prob lem cases The settings available in the Read Save or Jaguar Run windows are not what you expected them to be Many of the options for these windows 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 nei ther of those two files exists the default schrodinger hosts file for the local host is used You can find out which schrodinger hosts file is being used by clicking About in the Jaguar panel then clicking Schr dinger and looking at the con figuration file listed If you are using a different schrodinger hosts file than you expect or if you are working with a new version of Jaguar and a new schrodinger hosts file has been installed on your system you should examine the schrodinger hosts file for the job and make sure it is in the same form as the file for the system for the version of Jaguar that you are using and that the set tings are appropriate See Section 11 1 on page 263 for a description of the schrodinger hosts file 66 The job fails with a memory related error Memory fault out of memory or no memory available 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 whe
426. r the molecule in the gas phase are calculated The program ch performs electrostatic potential fitting which represents the wavefunction as a set of point charges on the atomic centers The interactions between the molecule and the solvent are evaluated by Jaguar s Poisson Boltzmann solver which fits the field produced by the solvent dielectric continuum to another set of point charges These charges are passed back to scf 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 energy for the molecule converges 112 Jaguar 5 5 User Manual Chapter 6 Output For solvation calculations on neutrally charged 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 molecule or system and assigns atomic van der Waals radii accordingly For more information on this process see Section 10 6 on page 253 These van der Waals radii are used to form the 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 lis
427. rational frequencies is requested with ifreq 1 and the level of theory being used is Hartree Fock IR intensities for the IR active vibrational modes are automatically calculated i e irder 1 automatically For DFT 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 Jaguar 5 5 User Manual 191 Chapter 9 The Jaguar Input File Table 9 25 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 optimization or from initial Hessian if initial Hessian was never updated maxitcp 35 Maximum number of CPHF iterations rmscp 5e 5 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 Quan tum Mechanical Force Fields SQM method 1 Scale frequencies using Pulay s SQM method and use scaled frequencies for thermochemical calculations only allowed for B3LYP calculations 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 cal
428. rbital 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 calcu lation 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 C1 C4 amp Jaguar 5 5 User Manual 217 Chapter 9 The Jaguar Input File For QST guided transition state searches with LMP2 wavefunctions 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 9 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
429. rd econv which gives the energy convergence criterion is set by default to 1 0 x 10 although if the calculation first satisfies the criterion dictated by the Methods keyword dconv the energy convergence criterion is ignored The keywords cfiterr wispc denspc and efield which are listed in Table 9 24 take on real values When charge fitting is constrained to reproduce multipole moments that is when incdip 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 190 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 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 elec trostatic 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 input an electric field for finite field polarizability and hyperpolarizability calculations as described earlier in this subsection Its default value shown in Table 9 24 applies to all cases when ipolar gt 1 For ipolar 1 3 point polarizability only calculations efield s default value is 0 006 au If you want to print out the electrostatic potential at grid points that you specify add the keyw
430. rd radprb in gen section of input file Jaguar 5 5 User Manual 59 Chapter 4 Options Table 4 1 Parameters for Various Solvents Solvent Dielectric Constant Probe Radius cyclohexane 2 023 2 78 carbon tetrachloride 2 238 2 67 benzene 2 284 2 60 chlorobenzene 5 708 2 72 1 2 dichloroethane 10 65 2 51 methanol 33 62 2 00 nitrobenzene 35 74 2 73 water 80 37 1 40 4 5 20 Performing or Skipping a Gas Phase Optimization If you are computing the solvation energy of a minimum energy or transition state struc ture 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 optimizations in solution are performed only after an optimized gas phase structure is computed However if you want only an optimized structure in solu tion and do not care about the accuracy of its computed solvation energy you can skip the gas phase geometry optimization by setting the Gas phase optimization option to no 4 6 Properties Various molecular properties can be calculated for a particular wavefunction These calcu lations are normally performed using the converged SCF wavefunction By default none of the properties listed below are computed but you can compute them by changing the settings in the Properties window which you open by clicking Properties 4 6 1 Electrostatic Potential Fitting Jaguar can fit the molecular e
431. responds 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 Jaguar 5 5 User Manual 261 Chapter 10 Other Jaguar Files 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 10 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 calculations 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 correspond to that desired for the molecule the keyword lewstr should be changed to correspond to a better structure as described in the gen section description in Section 9 5 on page 168 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
432. ret 33 Jaguar 5 5 User Manual iii Contents 3 4 Reading Piles uei arret rere E EEG IR Ee ER E ME ERE ENE AERE RU DN 34 34 1 Reading tn Geometries Only eerte tenere ern 34 3 4 2 Reading in Geometries and Job Settings sss 35 3 4 3 Read as Geometry 2 or Geometry 3 Settings sss 35 3 5 Cleaning up Molec lar Geometries euuus eene teet rteo vtta ero irte innare ener erise 36 3 5 1 Quick Geometry Optimization eet ertet etin 36 3 5 2 Sy mMM O 2 iere reete reete e REN ina DNUS BR E ep tees ES ERA 37 3 6 Running Jobs eei tere ree et e ERE Ra E EARTH EN LEHRER 38 3 6 1 Starting Individual Jobs tote ee tete eer rns 38 3 6 2 Running Batch Jobs Of SCrpts eise tenete tenete ieies 40 SNPs s 44 EMO UP P 45 3 9 Other Maestro Features eerie toten esten I eer RD Ee ber ree Eo cues 46 3 9 1 Checking Jobs With the Monitor Panel eese 46 3 9 2 The Rese ODUGI i nera rr E E sacs ASENT EUR 46 3 03 Sines DDDUEC aeree e ee UE celia teure HI eld OE e pen cakes 46 3 0 4 The About and Help ButtOns eter rrt ertet rhe 47 3 0 5 Closing the Jaguar Patiel e ertet e ee ai ene ees 48 3 9 6 Other Jaguar Panel Options erento etta eto ttn 48 Chapter 4 Opin vec coe restore euo tet eot eter enar ve e eea t Pra roseo tens eoe tore tt 49 4 1 Density Functional Theory DFT Settings seeeeeeee 49 44 1 Stage and Grid Density ee eterni
433. rizabilities 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 Idens 0 Do not calculate electron density 1 Calculate electron density on grid grid choice set by grid key word geldens ultrafine grid used by default 1 Calculate electron density on grid and write chdens file in a for Jaguar 5 5 User Manual mat 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 denspcz0 3 or smaller for best results 189 Chapter 9 The Jaguar Input File Table 9 23 Integer valued Keywords for Charge Fitting Multipole Moment and Polarizability amp Hyperpolarizability Calculations Cont d Keyword Value Description 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 Analytic polarizabilities 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 GAUSSIA
434. rning this option on you can choose to 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 6 5 File Output Options This section describes the options in the File Output window which you open using the File button in the Output section of the Jaguar panel These output options generate addi tional 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 from the File Output window the output from the program pre lists the non default options chosen This output appears above the molecular geometry output from the same program and indicates the non default values of the keywords referred to in footnotes throughout this section 12 Keyword ip8 2 in gen section of input file Jaguar 5 5 User Manual 129 Chapter 6 Output Gaussian 92 input deck g92 When this option is selected a file in the format of a GAUSSIAN 92 input file is created with the suffix g92 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 multiplicity of the molecule and any r
435. rocedure click OK to accept the geometry from the minimization Clicking Cancel discards the opti mized geometry and reverts to the initial geometry The convergence criteria for the cleanup minimization are deliberately set fairly loose so that even large systems can be optimized interactively In addition a time limit is imposed on the minimization to keep it from running excessively long As a result you might find Geometry Cleanup Molecular Point Group Cs Tolerance Fini Synunetiry Symmetrize molecule Clean up geometry OK Cancel Help Figure 3 5 The Geometry Cleanup window 36 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro 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 from Maestro s Build panel On the other hand performing a cleanup minimization 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
436. rt files jobname xx in where xx is a two digit number are displayed with the Hide mae files and Hide restart files options By default neither is displayed 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 Select Batch Inputs Input Dir zone1 dyalli Hiles benzene hf mae 7 carboxyindole 01 in benzene dft 01 mae fragmenti mon mae csearch out mae 1 10 phenanthroline in cyclohexane fuse best mae benzene dft mae benzene hf in benzene dft 01 plot in No input files selected Un Select all _ Hide mae files Hide restart files OK Cancel Hel Figure 3 9 The Select Batch Inputs window Jaguar 5 5 User Manual 43 Chapter 3 Running Jaguar From Maestro After you finish selecting the batch script and input files you can choose the host on which to run the job from the Job Host option menu If the host has more than one processor you can enter the number of processors to use in the CPUs text box The number of processors available is displayed to the right of this text box If you run the batch job on multiple processors the individual Jaguar jobs are distributed
437. rtup 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 12 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 SCHRODINGER environment variable you can run Jaguar jobs using the command SCHRODINGER jaguar It is usually more convenient to include the installation direc tory in your PATH or path environment variable so that you do not need to type SSCHRODINGER 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 your machine responded with 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 sh bash ksh export path installation directory path 282 Jaguar 5 5 User Manual Chapter 12 Troubleshooting 12 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
438. ructed from wavefunctions 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 e g 6 31G the initial guess is formed from the wavefunctions obtained from individual calculations on the atoms in the molecule which were calculated using that same basis set ignoring polarization and diffusion functions Therefore if you change the basis file you need to change the atomig file correspondingly and vice versa For other basis sets the wavefunctions used to construct the initial guess are obtained by projecting either the appropriate atomic wavefunction in default atomig onto the basis set actually being used for the molecular calculation The 6 31G wavefunction is used when ever possible when a 6 31G atomic wavefunction is not listed for a particular atom the MSV one is used for that atom For atoms beyond Xe in calculations using the LAV1S basis set the LAV2P atomic results are used 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 242 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files followed by one space and ending with the name or names separated by a space and or
439. ry of project based mouse functions is provided in Table 2 2 Table 2 2 Mouse Operations in the Project Table Task Select or include entry deselect or exclude all others Display Selection menu Select or include multiple entries Toggle entry selection or inclusion Move entry Mouse Operation Click Right click Shift click Control click Drag 2 8 Shortcut Key Combinations Some frequently used operations have been assigned shortcut key combinations The shortcuts their functions and their GUI equivalents are listed in Table 2 3 Table 2 3 Shortcut Keys in the Maestro GUI Keys Action Equivalent GUI Operation In the Main Window ALT B ALT C ALT E ALT H ALT I ALT M ALT N ALT O ALT P ALT Q ALT S ALT T ALT W ALT Z 16 Show build panel Create entry Show script panel Show help panel Show import panel Show measurement panel New project Open project Print Quit Show sets panel Show project table panel Close project Undo Redo last command Edit gt Build Project gt Create Entry From Workspace Edit gt Command Script Editor Help gt Help Project gt Import Structures Analysis gt Measurement Project gt New Project Project gt Open Project Maestro gt Print Maestro gt Quit Analysis gt Sets Project gt Show Table Project gt Close Project Edit gt Undo Redo Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface Table 2 3
440. s Same as setting ip11 3 but includes all possible angles regard less of atom connectivity Same as setting ip11 4 but includes all possible torsions regard less of atom connectivity Connectivity table Eigenvectors and eigenvalues of overlap matrix Overlap matrix One electron Hamiltonian Additional RwR information and DFT grid information All keyword settings including internal ones Multipole moments in atomic units and Debye Geometries in bohr as well as Angstroms Extra geometry optimization details Localized orbital locations and LMP2 pair energies for local LMP calculations full local LMP2 energy correction is sum of pair energies Fock matrix in Boys localized orbital space Extra optimization related information such as the quadratic energy error Same as setting ip192 2 but includes more detailed information such as the Hessian Numerical Hessian in freq output Diagonal force constants in internal coordinates 205 Chapter 9 The Jaguar Input File Table 9 31 Output Keywords and Their Settings Cont d Keyword Value Description 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 geometric mean of the corresponding off diagonal elements the value of the factor can be set using the opt194 keyword 4 AII diagonal and off diagonal force constants are printed a When any of the keywords is set equal to 1
441. s the current size is 4194304 pl 28583 p4 error alloc p4 msg failed 0 set the environment variable PA GLOBMEMSIZE whose default value under Linux is 4 MB to a larger number as the message suggests even if the amount of shared memory requested is less than the current setting The maximum value of the P4 GLOBMEMSIZE setting should be no larger than the maximum shared memory for the kernel For RedHat Linux 7 3 this is usually 33554432 bytes To see the maximum amount of shared memory your kernel can allocate enter the command cat proc sys kernel shmmax 13 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 POE no earlier than 2 4 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 296 Jaguar 5 5 User Manual Chapter 13 Parallel Jaguar If you see jmd processes listed you are running the Job Manager In this c
442. s C 3 protonation 0 2 0 2 36 Total RMS Deviation 0 7 306 Jaguar 5 5 User Manual Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group Chapter 14 The pKa Prediction Module MOLECULE pKa calc pKa exp Deviation ALCOHOLS methanol 16 4 15 5 0 9 ethanol 16 0 15 9 0 1 propanol 16 0 16 2 0 2 i propanol 15 8 17 1 1 3 2 butanol 16 8 17 6 0 8 t butanol 16 3 19 2 2 9 allylalcohol 15 3 15 5 0 2 propargylalcohol 13 4 14 3 0 9 2 chloroethanol 15 0 14 4 0 6 2 2 dichloroethanol 13 9 12 2 qd 2 2 2 trichloroethanol 12 6 12 4 0 2 2 2 2 trifluoroethanol 11 5 12 4 0 9 1 2 ethanediol 15 7 14 0 1 7 1 2 propanediol 15 4 14 9 0 5 1 3 propanediol 16 4 15 1 1 3 1 4 butanediol 16 4 15 1 1 3 PHENOLS phenol 9 8 10 0 0 2 4 aminophenol 10 6 10 2 0 4 4 chlorophnol 9 3 9 9 0 6 4 fluorophenol 9 5 9 4 0 1 4 methoxyphenol 10 4 10 3 0 1 4 methylphenol 10 3 10 5 0 2 4 nitrophenol 6 9 7 2 0 3 p xylol 10 4 10 3 0 1 4 hydroxybenzaldehyde 7 5 7 6 0 1 Jaguar 5 5 User Manual 307 Chapter 14 The pKa Prediction Module Table 14 2 Molecules Used in the pKa Parameterization Arranged by Functional Group MOLECULE pKa calc pKa exp Deviation CARBOXYLIC ACIDS cis 1 2 cyclopropanedicarboxylic 4 4 3 6 0 8 trans 1 2 cyclopropanedicarboxylic 4 1 3 8 0 3 cis 2 chlorobut 2 enecarboxylic 3 6 2 8 0 8 trans 2 chlorobut 2 enecarboxylic 3 3 3 2 0 1 2 chlorobut 3 enecarboxylic 3 0 2 5 0 5 2 chloropropanecarboxylic 3 3
443. s Jaguar runs a single point Hartree Fock calculation 3 2 Molecular Structure Input After you start Maestro the first task for any Jaguar calculation is to enter a molecular 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 3 4 on page 34 or you can enter and edit the geometry yourself using the Edit Geometry window This section describes how to create or edit a geometry using the Edit Geometry window and also describes the input formats for Cartesian and Z matrix geometries The geometries that you enter are displayed in the Maestro Workspace in which you can rotate and translate the structure edit the geometry display in various representations and perform many other tasks For information on using Maestro see Chapter 2 The geometry input is used to set constraints of bond lengths or angles for geometry opti mization and to specify atoms for a counterpoise calculation These aspects of geometry input are explained in this section as well 3 2 Entering or Editing a Geometry Using the GUI To enter or edit a geometry by hand or to examine the coordinates click the Edit button in the Geometry section of the Jaguar panel The Edit Geometry window is displayed If you have not read in a geometry file or created a geometry using Maestro you can type the geometry into the text entry area or cut and paste the geometry from another text
444. s 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 average 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 deproto nated state summing over all deprotonated conformations is equal to the total population of the protonated state also summing over all conformations This approach should be more accurate than that described in a although how important statistical effects are in practice remains to be ascertained 14 3 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 in our suite of test cases which has three equivalent sites In this situation there is a statistical correction factor arising from increased entropy of the appropriate species As we do not have an automated facility for recognizing equivalent sites in the current version of the program the user 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 parti cles involved H and the species being protonated For convenience
445. s as f10 5 labels in table all elements as f19 15 in list all elements as f8 5 in list all elements 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 31 Keyword ip102 in gen section of input file 32 This setting corresponds to having all of the orbital output keywords set to 1 33 Relevant orbital output keyword set to 2 3 4 5 or 6 in gen section of input file depending on the format setting chosen 34 Relevant orbital output keyword set to 7 8 9 10 or 11 in gen section of input file depending on the format setting chosen 35 Relevant orbital output keyword set to 12 13 14 15 or 16 in gen section of input file depending on the format setting chosen 36 Relevant orbital output keyword set to 2 7 or 12 in gen section of input file depending on which orbitals are printed 37 Relevant orbital output keyword set to 3 8 or 13 in gen section of input file depending on which orbitals are printed 38 Relevant orbital output keyword set to 4 9 or 14 in gen section of input file depe
446. s 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 which treats bonds as having equal amounts of covalent and ionic character allows GVB to describe charge transfer reactions and bond breaking and formation accurately and also gives better results for other molecular properties than an HF treatment alone can provide Jaguar 5 5 User Manual 149 Chapter 8 Theory The goal of a GVB calculation then is to obtain pairs of GVB orbitals Wha and V pps where p ranges from 1 to the number of GVB pairs N that lead to a minimum energy for the molecular wavefunction gvb N gvb Y L Y p V po pa OB Bo 4 p 1 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 computational 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 V pa V pp V pb 5 Vere 7 pa tS Sa E V pa 7 V pb 5b f2 5 The y orbitals generally have bonding character while the y orbitals are anti bonding The contribution to the GVB wavefunction from each pair is given by CoV pe pg C pu Su OB
447. s early and the output states you need a different number of lone pairs on a particular atom As described in Section 4 3 1 on page 57 286 Jaguar 5 5 User Manual Chapter 12 Troubleshooting and Section 7 1 2 on page 141 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 run ning the calculation again 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 con verge properly which may also lead to inaccurate calculation of molecular proper ties If you are performing a geometry optimization check to see whether the geometry changes are reasonable if you are performing a single point calculation make sure the structure entered is appropriate You might want to minimize the struc ture with a molecular mechanics program first If the structure is reasonable conver gence problems should not occur and we would appreciate it if you would describe them to us at the address given on page 319 preferably by e mailing us the input output and log files for the job with a brief explanation To get converged results in the meantime you can try using level shifting and or setting the accuracy level to ultrafine both of which are described in Section 4 9 4 on page 77 and Section 4 9 5 on page 78 The calculation will be slower but convergence may be better fo
448. s established that poor convergence of these systems is very often due to problems with the trial wavefunction s orbital shapes and occupations We have therefore developed an algorithm based upon ligand field theory that creates a high quality initial guess specifically designed for transition metal containing systems 19 The HF initial guess options labeled Ligand Field Theory and LFT dd repulsion both use this algorithm See reference 19 for further details Both initial guess methods can take advantage of user provided information on charges and spins of fragments within the system as described in Section 7 1 on page 139 although such information is not required If you restart a calculation with an input file generated during a previous run as described in Section 7 2 on page 142 the wave function from the earlier run is read from the guess section and used as an initial guess unless you change the default choice of Read from input The guess section is described in Section 9 10 on page 227 Jaguar can read in an initial guess in one basis set and transform it to the basis set requested for the calculation unless either basis set uses effective core potentials For GVB calculations the GVB initial guess options menu lets you choose the method used to generate this guess By default the GVB initial guess is automatically constructed from the Hartree Fock initial guess by piece wise localization Another option is t
449. s 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 316 Jaguar 5 5 User Manual Chapter 14 The pKa Prediction Module 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 Table 11 3 Table 11 4 and Table 11 8 14 5 4 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 14 3 Table 14 3 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 prt h input file preparation runs for conjugate acid dft B3LYP 6 31G geometry optimi
450. s the integer fragment label from the frag column of the atomic section To treat them all as dummy atoms make Jaguar 5 5 User Manual 225 Chapter 9 The Jaguar Input File 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 transi tion 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 set iopt420 420 in the gen section then manually assign ALL atoms to frag ments using the frag column of the atomic section The bonded metals must be assigned to separate fragments All atoms must be assigned because all unassigned atoms will be assumed to be in the same fragment Finally add formal and 2spin values in the atomic section 9 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 section Since for a Hessian H Hj Hj 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
451. s 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 calculations during the run use the RMS density change convergence criterion described in Section 4 9 on page 74 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed for several more iterations than single point energy calculations yield If you select forces only for the Optimize geometry setting the programs der1a rwr and der1b 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 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 calcula tions 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 1 O 0 000000E 00 0 000000E 00 2 620407E 05 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 Jaguar 5 5 User Manual 109 Chapter 6 Output When force calculations or optimizations of a system s minimum
452. scription in the file was of a carbon bound to a hydrogen the radius would be set to the radius matching that description even if a later line in the Lewis file described a carbon bound to three hydrogens 254 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files 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 recognized then lists atomic radii for various atom types The file contains different versions of this information for LMP2 calculations than it does for other wavefunction 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 is for HE DFT or GVB wavefunctions After all th
453. sed during the calculation to store temporary files You should check that the directory already exists on the calculation host If it does not exist you should create it If you read the input file from the samples directory the Job Directory is set to SSCHRODINGER jaguar vversion samples You must change it to some other direc tory because you normally would not have permission to overwrite files in this directory For this exercise choose the directory you were in when you launched Maestro You should not need to change any other settings Click the RUN button to start the job An alert box that contains information about the job is displayed After you start the job and dismiss the alert box the Maestro 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 6 8 on page 136 on the log file for more information on this data You can close the Monitor panel by clicking the Hide button If you want to reopen it later you can do so by choosing Monitor from the Applications menu in the Maestro main window When the job finishes its output file is copied to the directory specified in the Job Direc tory text box of the Jaguar Run window If you did not change this directory it is
454. selected eigenvector 31 Keyword ifollow 0 in gen section of input file 32 Keyword ifollow 1 in gen section of input file Jaguar 5 5 User Manual 91 Chapter 5 Optimizations and Scans 5 3 6 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 Jaguar travels on a potential energy surface in its search for an appropriate saddle point The QST 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 prop erly identified 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 following described in Section 5 3 5 on page 91 because any eigen vector selected for following should
455. ser Manual Chapter 8 Theory This chapter contains a description of some of the theory behind the methods used in Jaguar Section 8 1 describes the pseudospectral method itself Section 8 2 Section 8 3 and Section 8 4 describe GVB GVB RCI and LMP2 calculations and how the pseudo spectral method improves computational scaling and efficiency for these methods Section 8 5 contains a brief description of density functional theory Chapter 4 includes information about performing Jaguar calculations using the techniques described here 8 1 The Pseudospectral Method Like conventional ab initio electronic structure codes Jaguar solves the Schr dinger equa tion 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
456. ser Manual Chapter 11 Running Jobs Table 11 5 Input Format Keywords and File Types for Babel File Format Conversions Continued Format Keyword File Type dpdb feat fract gamout gzmat gauout g94 gr96A gr96N hin sdf jagin jagout m3d macmol macmod micro mm2in mmd2out mm3 mmads mdi molen mopcrt mopint mopout pemod pdb Jaguar 5 5 User Manual Dock PDB file Feature file Free Form Fractional file GAMESS Output file Gaussian Z Matrix file Gaussian 92 Output file Gaussian 94 Output file GROMOS96 A file GROMOS96 nm file Hyperchem HIN file MDL Isis SDF file Jaguar Input file Jaguar Output file M3D file Mac Molecule file Macromodel file Micro World file MM2 Input file MN2 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 273 Chapter 11 Running Jobs Table 11 5 Input Format Keywords and File Types for Babel File Format Conversions Continued Format Keyword File Type psin PS GVB Input file psout PS GVB Output file msf Quanta MSF file schakal Schakal file shelx ShelX file smiles SMILES file spar Spartan file semi Spartan Semi Empirical file spmm Spartan Molecular Mechanics file mol Sybyl Mol file mol2 Sybyl Mol file wiz Conjure file unixyz UniChem XYZ file XYZ XYZ file xed XED file Note that the format keywords are not used for file extensi
457. ser Manual 271 Chapter 11 Running Jobs 11 2 5 Converting File Formats Jaguar uses the Babel program 24 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 9 5 18 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 9 30 on page 201 the input format keywords are listed in Table 11 5 Table 11 5 Input Format Keywords and File Types for Babel 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 CHARM nm 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 272 Jaguar 5 5 U
458. settings shown are used for the run 5 Keyword isymm 0 in gen section of input file 38 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Jaguar Run Job Host localhost CPUs E Tayr iser 4 Job Dir Yzonet juliem test projects ne Comment w Cleanup Remove scratch directory zd RUN Cancel Help Figure 3 6 The Jaguar Run window If Jaguar is installed on more than one host at your location you can select a host to run the calculation from the Job Host option menu A temporary directory on the calculation host is used to store intermediate files during the calculation If there is more than one possible choice listed for the Tmpdir setting you should pick one A subdirectory with the given job name h2o for example is created within the temporary directory and the files from the calculation will be stored in this subdirectory If the subdirectory and directory do not have sufficient disk space for the job the job fails If your 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 list offers you different choices see Section 11 1 on page 263 The Job Dir setting is the local directory where input and output files created by Jaguar are written The defaul
459. sis set five dealiasing function sets are specified for each atom and that each of these sets contains dealiasing functions for a total of six 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 coefficient is being evaluated is to be approximated by short range dealiasing functions then the dealiasing functions for first order neighbors 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 functions 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 fo
460. sisse 20 319 temperatures for thermochemical calculations keywords for ses 192 OUEDUL i coris tote rte ies 122 Settng iuaneaeomdnpiinietei 69 temporary directory 39 40 285 after job is killed 271 errors related to 284 285 in output file eese 102 saving at end of job 270 specifying in hosts file 265 266 temporary files eeeee 40 271 saving at end of job 270 thermal smearing eee 197 thermochemical properties 5 00 keywords for sse 192 OULPUL i oie teo teintes 122 time stamps in log file option for 270 timex prOBratm e eerte tnn enini 233 timing information keyword for eese 204 Option TOR s n 125 toolbar Maestro s es 11 torsional angles in Z matrix 30 torsions freezing all s 86 transition metals improving convergence 76 77 139 141 initial guess for 76 226 transition state optimization 83 94 constraining bond lengths or angles ees 86 181 convergence criteria 84 85 183 convergence criterion for SCF 84 eigenvector following 91 182 183 frozen bond lengths or angles 86
461. st 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 described below In this fashion all of the errors associated with the various components of the method are subsumed into a small number of parameters characteristic of the functional group in question 14 2 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 impor tant 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 methodology For the molecules considered below it appears to be quite satisfactory For example for protonation of nitrogens in heterocycles an average predic tion accuracy of 0 19 is obtained over 16 molecules whose pK values range fro
462. st 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 If you want to perform an open shell singlet calculation using UDFT or UHF you must use iopt457 457 to set up an initial guess and also set isymm 0 and iuhf 1 This option replaces the alpha and beta HOMO with a mixture of the HOMO and LUMO as follows Q HoMo yomo PLumo 2 ouovo PhHomo Prumo 2 The orbitals are taken from a closed shell starting guess The LUMO remains the same Note This starting guess does not correspond exactly to the open shell singlet state but is a mixture of singlet and triplet states The final wave function in a UHF calculation will not necessarily correspond to what would be obtained in a 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 Jaguar 5 5 User Manual 199 Chapter 9 The Jaguar Input File 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 9 5 17 Localization Keywords For any Jaguar job the final wavefunction can be localized after it
463. 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 subsequent 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 structures 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 other coordinates This process is well defined and straightfor ward 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 20 Keyword iqst 0 in gen
464. struction of 175 standard functional names 174 DFT see density functional theory dielectric constant Keywords for sees 188 setting in the Solvation window 59 dielectric continuum method see pbf program DIIS convergence scheme 17 105 137 keyword for coefficient output 208 keywords for dipole moment see multipole moments Direct Inversion in the Iterative Subspace meth od see DIIS convergence scheme directory changing in Maestro eee 6 current working eseeeeenee 6 file output etre 18 displacement convergence criteria based on 84 keywords for convergence criteria 184 DISPLAY environment variable 3 283 display host sss 281 283 284 driver for geometry scan 93 94 ASOLV program ener tes 233 dummy atoms in the Hessian eects 226 in Z matrix input esee 31 E echo input file section sss 231 ECPs see effective core potentials Edit Geometry window af Edit window sss 26 28 fixing bond lengths or angles 32 fixing Cartesian coordinates 29 freezing bond lengths or angles 86 87 freezing Cartesian coordinates 86 87 editing geometries from Maestro 26 28 editing input files from Maestro
465. t 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 example the input Oo 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 3 2 3 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 Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 75
466. t For optimization steps past the first geometry change the change in total energy from the previous geometry to the newly calculated 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 the previous paragraph are important because they are each tested against the convergence criteria determined by the Convergence criteria setting from the Optimization window as described in Section 5 1 on page 83 or alternatively the criteria set by the gconv keywords in the input file The criteria are described in detail in Section 9 5 9 on page 179 If the gradients are converged and the energy change is below 2 5 x 107 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
467. t in the Monitor panel and incorporate the results Monitored jobs are incorporated only if they are part of the project You can monitor jobs that are not part of the project but their results are not incorporated To add their results to the project you must import them Jaguar 5 5 User Manual 19 Chapter 2 The Maestro Graphical User Interface etot etot etot etot etot etot etot scf HF done Job benzene hf completed on faith schrodinger com at Thu Jul 3 13 27 12 2003 Monitor monitor i i ej xj RMS maximum energy density DIIS total energy change error na 230 05373319386 B 230 55368060465 6 0E 01 2 230 70348819089 5 0E 02 6 230 70781618941 4 3E 03 5 230 70816276266 3 5E 04 9 230 70846878103 3 1E 04 7 230 70847726109 8 5E 06 0 lt z lt z lt lt zZz tabs PNONDDN rons zczxczxxx oan zum Figure 2 7 The Monitor panel 2 13 Help Maestro comes with automatic context sensitive help Auto Help Balloon help tool tips an online help facility and a user manual To get help follow the steps below 20 Check the Auto Help text box located below the title bar of the main window If help is available for the task you are performing it is automatically displayed there It describes what actions are needed to perform the task If your question concerns a GUI element e g a button or option menu there may be Balloon help for the item Move the mouse poi
468. t you can use variables to keep several atoms within the same plane during an optimization by setting their coordinates along one axis to the same variable To use variables to set coordinate values from the Edit Geometry or Edit Job window first type the variable name zcoor for instance where you would normally type the corre sponding numerical value for each relevant coordinate You can put a or sign immedi ately 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 Jaguar 5 5 User Manual 87 Chapter 5 Optimizations and Scans For instance in a geometry optimization using the following Cartesian input Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoorz0 753108 zcoor 0 454006 the H atoms remain in the same xy plane and the same xz plane the molecular symmetry is preserved Whenever Cartesian input with variables is used for an optimization Jaguar performs the optimization using Cartesian coordinates rather than generating redundant internal coordi nates and the optimization does not make use of molecular symmetry 5 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 advantag
469. t File 9 5 6 LMP2 Keywords The mp2 keyword allows you to request a local Moller Plesset perturbation theory LMP2 calculation By default LMP2 is off mp2 0 For more information on the local MP2 method see Section 4 2 on page 54 and Section 8 4 on page 156 LMP2 keywords are given in Table 9 7 LMP2 calculations require a basis set that allows the pseudospectral method to be used See Table 4 3 on page 71 and Table 4 4 on page 73 to obtain this basis set information Local MP2 calculations use the LMP2 method for all atoms unless the Imp2 section described in Section 9 7 on page 217 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 9 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 loclmp2v as indicated in Table 9 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 Table 9 7 Keyword Settings for Local MP2 Calculations Keyword Value Description mp2 0 Do not run local second order Mgller Plesset perturbation theory LMP2 calculation 1 Correlate core and valence electrons 3 Run LMP2 calcul
470. t 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 func tional groups However parameterization of the model for ionic species in this fashion cannot lead to high levels of accuracy because there are large error bars on the experi mental 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 cancellation of two very large terms the gas phase deproto nation energy which favors the protonated 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 we have adopted a novel strategy which is to fit the parameters for ions directly to experimental pK data If the gas phase quantum chemistry and neutral solvation are reliably computed then the solvation 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 i
471. t file for a calculation 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 restart file for an IRC job includes the geometry of the last found IRC point This geometry is in the zmat section An iremode downhill setting is included in the gen section regardless 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 186 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File 9 5 11 Solvation Keywords Most of the solvation keywords correspond to GUI options described in Section 4 5 on page 58 The allowed values for the integer solvation keywords are described in Table 9 21 Defaults for these keywords are not indicated in bold italics since the keyw
472. t given here is in points bohr xmaxadj 0 0 Amount to adjust the box boundary on the x axis Can be posi tive or negative xminadj 0 0 Amount to adjust the box boundary on the x axis Can be posi tive or negative xadj 0 0 Amount to adjust the x dimension of the box Half the adjust ment 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 posi tive or negative yminadj 0 0 Amount to adjust the box boundary on the y axis Can be posi Jaguar 5 5 User Manual tive or negative 215 Chapter 9 The Jaguar Input File Table 9 40 Keywords for Generating Plot Data Cont d Keyword Value Meaning yadj 0 0 Amount to adjust the y dimension of the box Half the adjust ment 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 posi tive or negative zminadj 0 0 Amount to adjust the box boundary on the z axis Can be posi tive or negative zadj 0 0 Amount to adjust the z dimension of the box Half the adjust ment is added to each boundary Can be positive or negative plotfmt vis Set the format and file extension for plot files to vis the default Maestro format plt Set the format and file extension for plot files to p1t 9 6 The gvb Section The gvb section whose GUI equivalent is described in Section 4 3 on page 56 is not keyword based The section should co
473. t 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 You can change the default selection by editing the directory name If the job host you choose is identified in the schrodinger hosts file as having more than one processor you can run Jaguar in parallel on that host When you choose a multi processor host the of Processors section becomes active and the number of processors available is displayed to the right of the text box To select the number of processors on which to run the job change the value in the text box The default is one processor The text in the Job name box determines the names of many of the files created by Jaguar as well as the name of the subdirectory within the temporary directory which is described Jaguar 5 5 User Manual 39 Chapter 3 Running Jaguar From Maestro above The files whose names depend on the job name include the input file the log file which shows the job s progress and the output file listing the calculation results For instance if the job name is h2o the results are stored in a file called h20 out within the local job directory The default setting for the job name is the base of the input file name if any from which the molecular geometry was read For example if you read the geometry from a file called h201 in the default job name setting would be h201 You can change the job name in Job n
474. tailing the number of electrons in the molecule the number of alpha and beta electrons the total number of orbitals for the calculation the numbers of core open shell occupied and virtual orbitals the number of Hamiltonians used for the calculation the number of shells and the calcula tion 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 itera tion 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 104 Jaguar 5 5 User Manual Chapter 6 Output 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 calcu lated 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 indi cates 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 hea
475. te 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 conver gence criterion which is described in Section 4 5 on page 58 If the solvation energy has Jaguar 5 5 User Manual 115 Chapter 6 Output 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 6 3 8 Geometry Optimization in Solution Geometry optimizations in solution contain output in the formats described in the previous two subsections but the optimization output and the solvation calculation output alter nates 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 optimi zation Next the SCRF procedure is used to compute a wavefunction for the solvated system as for a single point solvation energy calculation When the solvation energy has converged
476. te eth innt ene in dude 66 4 7 4 Animation of Frequencies tereti ttet eae rens i ertet doe 67 47 5 Diitr red Intensit s reden etit trt Ere tate cer tee PR RP HERE SER 69 4 7 0 Thermochemical Properties emeret 69 4 8 BASIS SOb m 70 49 Methods cR 74 4 9 1 Wavefunction Type Restricted or Unrestricted sss 74 4 9 2 Selecting Bletronig States oie eret ertet ee ete e ede tea 75 4 9 3 Choosing an Initial Guess Type eerte tereti ttr etes 76 4 9 4 Convergence ISSUES 2s uoce tereti teret hereto rte aeree etri pep indo 77 4 95 A cc rdcy Level tee ete eerte ie Fieri as IEEE 78 4 9 6 Analytic COPTGCHOfIS asore eere trt entree titt reae enero ret reete rene eere ei 78 4 9 7 Final Localization of the Orbital mte 79 LR EEUU e 79 4 10 Surfa ES E E 79 4 11 J2 Eheory Calculatlols s ce eere toners erento ren E O EEE EE E EEEa R EE cds 81 Chapter 5 Optimizations and Scans esee eere eene eee eese tatnen snnt 83 5 1 Geometry Optimization The Basics sese 83 5 1 1 Maximum Iterations suci tete ctr eret rti eite re Rehd 83 5 1 2 Geometry Convergence ISSUE soisin rer Pes eden E PEE 84 5 1 3 The Enstial Hessian oer ce ertet eet eer reete Hec nn 85 5 1 4 Trust Radius in eI EHERREUHER NI HEINE S 85 5 2 Constraumng Coordinates escena ana er teer etat i oet te pee RU a
477. teration and the process continues until both the GVB natural orbitals and the CI coefficients have converged The GVB treatment can also be applied to open shell cases or restricted to certain electron pairs These variations are described in reference 20 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 8 3 GVB RCI Wavefunctions The GVB RCI restricted configuration interaction wavefunction is the simplest multide terminantal reference wavefunction which 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 important 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 wavefunction is used as a corre lated mean field reference state 12 This implementation of GVB RCI can be used to generate highly accurate GVB RCI wavefunctions with en
478. terations whose number is istavg revise orbitals so that they correspond to average of density matrices from preceding and cur rent 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 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 for 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 40 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 196 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 27 Integer Keywords for Methods Used in the SCF Convergence Procedures Cont d Keyword Value Description ifdtherm 0 Do not use thermal smearing in DFT or HF calculations 1 Use fractional occupation number FON method for thermal
479. terpreting the input file In this document to type a command means to type the required text in the specified loca tion and to enter a command means to type the required text and then press the RETURN key 1 2 Citing Jaguar in Publications The use of this program should be acknowledged in publications as Jaguar 5 5 Schr dinger L L C Portland OR 1991 2003 Jaguar 5 5 User Manual 3 Chapter 1 Introduction 4 Jaguar 5 5 User Manual Chapter 2 The Maestro Graphical User Interface Maestro is the graphical user interface for all of Schr dinger s products FirstDiscovery Glide Impact Liaison and QSite Jaguar MacroModel Prime and QikProp It contains tools for building displaying and manipulating chemical structures for organizing loading and storing these structures and associated data and for setting up monitoring and visualizing the results of calculations on these structures This chapter provides a brief introduction to Maestro and some of its capabilities For more information see the Maestro User Manual Most Maestro panels are amodal more than one panel can be open at a time and a panel need not be closed for an action to be carried out Instead of a Close option in one of the panel menus each Maestro panel has a Hide button so that you can hide the panel from view 2 1 Starting Maestro In order to launch Maestro you must first set the SCHRODINGER environment variable to point to the inst
480. text box in the Save window or in the Job Name box in the Jaguar panel If you did not read in the geom etry from a file you should enter a job name in either the Save window or the Jaguar panel You can save files in a variety of formats for other programs using the Save as menu For any file formats other than the Jaguar input in file only the geometry is included in the file Jaguar uses the Babel program for the file format conversions see Section 11 2 5 on page 272 The file name is determined by appending the extension indicated in the file type list to the job name Any text entered in the box marked Comment appears in the input file for the job If you symmetrize the geometry see Section 3 5 2 on page 37 the comment notes that the geometry was symmetrized to a certain point group You can type other text describing the job for your own convenience The comment cannot contain the characters or amp The comment appears in the Jaguar input file immediately above any keyword settings corre sponding to other selections 3 8 Output A Jaguar log file contains comments on the progress of a job If the job was started from the GUI the log file is written to the local job directory selected in the Run window 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 lau
481. th the extensions for the file names listed which can be changed by editing the Filter text box but also determines the format the file is expected to have Also make sure the file name and not just its directory is really showing up in the Selec tion text box before you click OK See Section 3 4 on page 34 for more information The molecular structure for the calculation is not what you expected it to be If you read in a Jaguar input bgf hes dat or GAUSSIAN 92 input file or if you read in a file containing only a geometry the geometry is obtained from that file unless you edit the geometry after reading the file Any geometry you entered before read ing the file is erased Also if you symmetrize the geometry or set symmetry on for the calculation as described in Section 3 5 2 on page 37 Jaguar may make small changes to the molecular geometry If these changes are a problem you should avoid symmetrizing the geometry and 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 or a GAUSSIAN 92 input file some of the settings in the file take precedence over set tings previously made in the GUI See Section 3 4 on page 34 for more details Also certain settings affect other settings automatically for instance if you choose to calculate polarizabilities the energy convergence criterion can be reset to 1 0 x 10 For a GVB job the program exit
482. th the predicted pK being too low acidic by about 3 pK units We believe the source of this error to come from the oversta Jaguar 5 5 User Manual 305 Chapter 14 The pKa Prediction Module bilization of the ionized form CH4 CO It is possible that the continuum solvation model does not fully account for the steric shielding from the three methyl groups on the negatively charged oxygen For functional groups where a relatively small number of compounds have been included in the parameterization the results are obviously less reliable We have nevertheless included some groups of this type hydroxamic acids sulfinic acids sulfonic acids thiophenol and imine in the initial release Feedback in these cases as to the validity of the parameterization would be particularly valuable to us in developing the next generation of parameters Table 14 1 Functional Groups for Which pKa Parameters Are Available Maximum jres File RMS Absolute Group Functional Group Deviation Deviation Number Alcohols 1 2 2 9 1 Phenols 0 3 0 6 2 Carboxylic acids 0 6 1 5 4 Thiols 0 2 0 4 10 Sulfonamides 0 6 1 5 15 Hydroxamic acids 0 6 1 5 6 Imides 0 9 1 4 13 Barbituric acids 0 4 0 6 12 Tetrazoles 0 7 1 4 17 Primary amines 0 5 0 9 31 Secondary amines 0 5 0 8 32 Tertiary amines 0 8 1 4 33 Anilines 0 3 0 6 25 30 Amidines 0 4 0 5 22 Heterocycles 0 3 0 5 19 Benzodiazepines 0 7 1 6 23 Guanidines 0 7 1 4 21 Pyrroles C 2 protonation 0 6 0 9 35 Indole
483. 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 260 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files 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 information for that element see Section 10 6 2 on page 256 for more information while the rightmost 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 Gro
484. 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 1 echo section constructed and keywords mtest 2 and ip24 2 in gen section of input file 2 Keyword ip5 2 in gen section of input file 124 Jaguar 5 5 User Manual Chapter 6 Output values for the number of arrays their size in 8 byte words and their size in bytes as well as the type of variables 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 seconds spent in various Jaguar programs is listed in the 3 output geometries in atomic units also This option allows you to choose 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 Properties window this option allows you to choose to list them in the output file in
485. the energies describes the relations 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 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 107 The virtual orbitals are obtained by diagonalizing 7 f 2J K where f is the occupation of each orbital 1 for a closed shell For closed shell Hartree Fock calcula tions this definition yields the standard orbitals and eigenvalues Jaguar 5 5 User Manual 105 Chapter 6 Output Finally the CPU time for the job the machine upon which the job ran and its time of completion are noted at the end of the output file 6 3 Output File Content for Calculation Options 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 molecul
486. 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 10 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 functions span the function space determined by the grid more completely than the basis functions so 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 func tions which is determined 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 basis function is centered and the atom upon which the short range dealiasing Jaguar 5 5 User Manual 243 Chapter 10 Other Jaguar Files 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 d
487. the output Error creating or cd ing to temp directory scr erwin h2o appeared in the h20o 10g 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 284 Jaguar 5 5 User Manual Chapter 12 Troubleshooting You might need someone to create the appropriate temporary directory or change permis sions on it from the root account Use the command 1s 1 to get information on owner ship 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 12 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 by selecting OK in the Run window as described in Section 3 1 on page 23 and Section 3 6 on page 38 the rsh command is not being allowed This problem may occur even if the job submission host the local host and the host where the cal
488. the unlikely event that you wanted to enter this Hessian 11 21 31 41 51 61 71 81 91 21 22 32 42 52 62 72 82 92 31 32 33 43 53 03 73 83 93 41 42 13 44 54 64 74 84 94 51 52 53 54 55 65 75 85 95 61 62 63 64 65 66 76 86 96 71 72 73 74 75 76 7 87 97 81 382 383 84 85 86 87 388 98 91 92 93 94 95 96 97 98 99 you would need to enter the elements from the bottom triangle of the Hessian shown in bold in the following way amp hess g d 11 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 i 81 82 83 84 85 i 91 92 93 94 95 j i 66 i 76 y i 86 87 88 i 96 97 98 99 amp where i and j indicate integer labels not actually used by the program In fact the lines containing j can contain more than one integer as described above 9 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 Jaguar 5 5 User Manual 221 Chapter 9 The Jaguar Input File 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
489. ting of non default options See Section 9 8 on page 218 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 energy breakdown for the scf output also describes the electron nuclear and kinetic contributions to the total one electron terms in the energy as well as the virial ratio V T where V is the potential energy and T is the kinetic energy This ratio should be 2 if the calculation satisfies the virial theorem After the first scf 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 6 3 9 on page 116 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 information on the area in A 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 surfac
490. 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 eigenvalues of the overlap matrix are discarded until there are ncanorb orbitals left Setting ncanorb sets icanorb to a positive value 9 5 16 Initial Guess Keywords Table 9 28 lists the keywords related to the initial guess and the meaning of the integer values each keyword can take on Most of the keyword values in Table 9 28 correspond to options described in Section 4 9 on page 74 Table 9 28 Initial Guess Keywords Keyword Value Description igonly 0 No effect 1 Use initial guess or input wavefunction for any post SCF calcu lations skipping SCF step iguess 0 Generate initial guess by diagonalizing one electron Hamilto nian 1 Read initial guess from guess section from input file or from guess file specified in WAVEFNFILE line iguess 1 automati cally if input file contains non empty guess section 10 Construct initial guess from orbitals which give best overlap with atomic orbitals in default atomig or other atomig file listed in in
491. to the defaults Clicking Reset clears the geometry and data from any other files read in as well as all settings describing the wavefunction and properties to be calculated and any settings you may have made using the Geometry or Output buttons It also sets the Job name value in the Run or Save window to whatever is appropriate when you read or enter the next geometry However the other selections you have made in the Run or Save window remain the same Reset prompts you to confirm or cancel the operation 3 9 3 Editing Input The Edit Input button in the Job Name section opens the Edit Job window which allows you to make changes to the entire input file However you cannot change between Z matrix and Cartesian input formats in this window Geometry input format conversion can be done only in the Edit Geometry window The editing options in the Edit Job window are the same as in the Edit Geometry window See Section 3 2 1 on page 26 for more details Changes you make in the Edit Job window are not saved to disk until you click OK in the Run window or the Save window 46 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Edit Job zifeni x File Edit Z matix Structure entry name benzene inc2 inc3 amp gen amp amp zmat c 1 4061490000000 7030750000000 0 7030750000000 1 4061490000000 0 7030750000000 7030750000000 4991970000000 2495990000000 1643680000000 1 2495990000000 1643680000000
492. tory used for the job would be temp erwin h2o By default Jaguar removes this subdirectory when the job is completed after copying back all important files to the output directory unless the subdirectory already existed when the job started Jaguar 5 5 User Manual 265 Chapter 11 Running Jobs You can override the tmpdir setting in the schrodinger hosts file by setting the SCHRODINGER TMPDIR environment variable For example if the directory designated by tmpdir becomes full with files that you don t have permission to delete you can set SCHRODINGER TMPDIR to a different directory and continue to run Jaguar jobs Instead of using tmpdir or SCHRODINGER TMPDIR you can directly specify the full path to the scratch directory in the JAGUAR SCRATCH environment variable 11 1 4 The processors Setting For stand alone computers with multiple processors set processors to the number of processors in the computer For computer clusters set processors for each node to the total number of processors in the entire cluster 11 2 The jaguar Command You can use the jaguar command to perform the following tasks among others 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 Listthe jobs that are running on a particular machine If Jaguar is installed on more than one machine at your site you
493. tracted to form a double zeta basis and LAV3 that all of the s functions and the last p and d Gaussian have been uncontracted 72 Jaguar 5 5 User Manual Chapter 4 Options Table 4 4 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 91 92 LAV2D Na La Hf Bi H Li Ne D95V H Li Ne 91 92 LAV2P Na La Hf Bi H Ne 6 31G H Ne 91 92 H Ne LAV3D Na La Hf Bi H Li Ne D95V H Li Ne 91 92 LAV3P Na La Hf Bi H Ne 6 31G H Ne 91 92 H Ne LACVD K Cu Rb Ag H Li Ne D95V Na Ar H Li Ne 93 Cs La Hf Au Zn Kr Cd Xe Hg Bi LAV3D LACVP K Cu Rb Ag H Ar 6 31G Zn Kr x H Ar 93 Cs La Hf Au Cd Xe Hg Bi LAV3P H Ar LACV3P K Cu Rb Ag H Ar 6 311G Zn Kr H Ar 94 Cs La Hf Au Cd Xe Hg Bi LAV3P H Ar plus metal diffuse d CSDZ Ce Lu H Ar 6 31G Zn Kr x H Ar 95 Cd Xe Hg Bi LAV3P H Ar K Cu Rb Ag Cs La Hf Au LACVP ERMLER2 K Lr H Ar 6 31G c H Ar 96 103 Ga Kr In Xe TI Rn 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 basis set used for atoms not described by ECPs S indicates the STO 3G basis set D indi cates the D95V basis set and P indicates the 6 31G set developed
494. transition state you might want to refine the Hessian used for the job 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 5 3 6 on page 92 The Hessian can be refined in both ways in the same job If you put an asterisk after a coordinate value Jaguar will compute 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 optimization 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 line at the end of the geometry input that defines the variables For instance if you entered either of the following two input geometries in the Edit window ol H2 O1 1 T7 H3 O1 L 25 H2 108 0 or O1 H2 O1 ohbond H3 O1 ohbond H2 108 0 ohbond 1 1 they would have the same effect a job from either input that included Hessian refinement would use both O H bonds and the H O H angle in the refinement Molecular symmetry or the use of variables either of which may constrain several coordi nate values to be equal to each other can reduce the number of coordinates actually used for refinement For example for the second water input example shown above only two coordinates will actually be refined the
495. tric 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 qi E rj 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 Jaguar 5 5 User Manual 229 Chapter 9 The Jaguar Input File 9 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 calculations The electronic energy is given by the equation E M fhu Yai i Ep i ij where the sums are over orbitals 20 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 h The terms a and b 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 mole cule Next each shell is described in turn The first line of each shell description should contain two numbers the first an
496. tructures or solvated transition states To perform a geom etry optimization in solution you must make appropriate settings in the Optimization window as well The solvation energy from a geometry optimization is computed as the difference between the energy of the optimized gas phase structure and the energy of the solvated structure that was optimized in solution In the SCRF method that Jaguar uses Jaguar first calculates the usual gas phase wavefunc tion and from that the electrostatic potential and fits that potential to a set of atomic charges as described in Section 4 6 1 on page 60 These charges are passed to the Jaguar 29 Keyword isolv 2 in gen section of input file 58 Jaguar 5 5 User Manual Chapter 4 Options Solvation Dielectric constant 2 023 Solvent molecular weight 4 16 Solvent density 0 77855 The probe radius is 2 777 Gas phase optimization yes OK Cancel Help Figure 4 4 The Solvation window 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 mechan ical wavefunction calculation incorporating the solvent charges This process is repeated until self consistency is obtained The cost is roughly
497. try 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 outputs the numerical first derivatives in a force table similar to the usual geometry optimization force table described earlier in this section The output then lists the matrix indices of the most asymmetrical Hessian element before symmetrization Jaguar 5 5 User Manual 121 Chapter 6 Output The symmetrized numerical Hessian is not printed in the output but can be found in the restart file which is discussed in Section 7 2 on page 142 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 entropy 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 i
498. try B2 1 000000 Symmetry A1 00000 0 00155 0 00430 0 00000 0 00000 0 00000 0 00000 0 00000 0 00000 0 00034 0 00034 0 00000 0 00037 0 00025 345597 Occupation 00019 00000 1 000000 Symmetry A1 00000 0 08586 0 41777 0 00000 0 00000 0 00000 0 00000 0 00000 0 14851 0 01307 0 01307 0 00000 0 02205 0 01342 713206 Occupation 03150 00000 1 000000 Symmetry B2 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 136 Jaguar 5 5 User Manual Chapter 6 Output For the table of SCF iteration information 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 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
499. ts file 263 265 287 hij 319 launching uei ie tits 3 main WIDdOW i soca cesectensiedicutosecivaness 7 Monitor panel s 25 40 problems starting 283 284 Scratch project scscisesscsecsesseeescedeesesecseesvees 7 masses for frequency calculations 66 input keyword for 169 setting in atomic section 218 220 memory keywords for sss 212 213 troubleshooting related to 287 memory usage keywords 212 337 Index memory disk and i o information keyword for sse 204 output option sssr 124 125 Methods window ss 74 79 accuracy level tact PR 78 analytic corrections ssss 78 convergence issues sss 771 718 initial guess selection in 76 77 keywords for usss 193 197 localization of orbitals 79 output from seen 123 131 symmetry use of sss 79 wavefunction type selection in 74 minimum energy path MEP calculations 95 Molden orbitals file mo1 keyword for 207 molecular charge keyword fof ssia iiir 169 setting for ao molecular properties eee 60 calculating eire 60 64 output wo eects 116 121 molecular st
500. ts 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 polarizability and or first hyperpolarizability of the molecule the output includes data from all the SCF calculations involved See Section 4 6 on page 60 for details on the methods used to calculate polarizability and hyperpolarizability The data from the program scf includes the virial ration V T 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 calculation 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 I I 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
501. tten then start Maestro by entering the command Jaguar 5 5 User Manual 23 Chapter 3 Running Jaguar From Maestro Jaguar fen xg Save Hide About Help Geometry State Geanup Edit Structure C2H40 neutral singlet Output Standard Files Per Iter Orhitals Jobs Run Batch Surfaces Reset Job Name aldehyde Edit Input DFT Optimization Solvation Local MP2 Properties Basis Set GVB Frequencies Methods Figure 3 1 The Jaguar panel SSCHRODINGER maestro If SSCHRODINGER is in your PATH you can simply type maestro Once Maestro is running choose Jaguar from the Applications menu to open the Jaguar panel 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 use the Edit Geometry window Click the Edit button then click in the text entry area in the Edit Geometry window and type the following lines Oo 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 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 sepa rate different items When you finish entering the water geometr
502. ty grids are also available The other settings determine the functionals used if any Unless you select a functional or functionals no DFT calculation is performed 1 Keyword dftname in the gen section of the input file selects functionals for the SCF calcula tion 2 Keyword jdft in the gen section of the input file selects post SCF functionals 3 Keywords gdftmed 10 gdftfine 11 and gdftgrad 12 in gen section of input file 4 Keywords gdftmed gdftfine and gdftgrad 13 in gen section of input file 50 Jaguar 5 5 User Manual Chapter 4 Options 4 1 2 DFT Model Options The most commonly used functionals can be selected from the DFT Model option menu Below this menu are four option menus that allow you to select local and nonlocal exchange functionals and local and nonlocal correlation functionals When you make a selection from the DFT Model menu the selections in these four menus change accord ingly By default DFT is not used so the default settings are none The DFT Model options include both pure DFT methods and hybrid methods 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 27 28 Becke 3 or the parameters developed for Becke s Half amp Half method 26 The option menu also contains some recently developed hybrid and non hybrid functionals
503. uar 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 the troubleshooting information in Section 12 2 on page 286 Memory use keywords are listed in Table 9 38 along with their default values and a description of their uses If you want to change some memory use but do not have a detailed knowledge of the code do not change the variables mxpr or mxrwr 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 store it on disk Names and default values in bold italics for these keywords are indicated in Table 9 39 If a grid is 212 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File Table 9 38 Keywords Related to Memory and Disk Use Keyword Default Description mxstrip 200 Information for matrix elements evaluated on basis func tions 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 program scf memory is allocated ngblok mxpage words at a time as needed where ngblok is a parameter currently set to 128 nbuck 64 Gridblocks are split up into sub gridblocks whose points are all on the same atom and in the same region of space with at most nb
504. uar input files as described in Section 3 4 on page 34 and run jobs from the GUI as described earlier in this section Alternatively you can use a Jaguar input file as input for a job submitted from the command line You must start jobs from the command line if you cannot display the GUI on your monitor or terminal For information on submitting jobs from the command line see Section 11 2 on page 266 Jaguar input files can be copied to other machines that have Jaguar installed and used for runs there In the Save window which you open by clicking the Save button in the Jaguar panel the Input file directory is the directory on the local host in which the file is written The default input file directory is the directory from which you most recently read a file if you read one or the directory you were in when you started Maestro You can set the directory by typing the name in the Input file directory text box 44 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Input file directory zone1 juliem jaguartest Job name benzene inc2 inc3 save as Figure 3 10 The Save window The Job name text determines the name of the input file created by Jaguar For instance if the job name is h20 and you save a Jaguar input file this file is named h20 in The default setting for the job name is the stem of the input file name if any from which the molecular geometry was read You can change the job name in Job name
505. uar 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 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 270 Jaguar 5 5 User Manual Chapter 11 Running Jobs To run a Jaguar job on the machine hostname with a particular non default set of executa bles you can use the command jaguar run HOST hostname VER version jobname 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 11 4 For example jaguar 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 subm
506. uck 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 them selves ndisk 1500 Atomic strips of 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 mxpr mxrwr 100 Maximum number of dealiasing functions evaluated at a time in subroutine rwrcalc zmpmem 1 0 For LMP2 single point and gradient code maximum total size allowed for arrays holding partially transformed inte grals on grid is 60 MB x zmpmem 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 Note If you set iqgrad you must set iqufine to the same value Jaguar 5 5 User Manual 213 Chapter 9 The Jaguar Input File Table 9 39 Keywords to Determine When to Comput
507. uestions page located at http www schrodinger com Support faq html The manuals and the release notes are available in PDF format from the Schr dinger web site at http www schrodinger com Support pdf html Information on additions and corrections to the manuals is also available from this web page If you have questions that are not answered from any of the above sources contact Schr dinger using the information below Schr dinger E mail help schrodinger com USPS 1500 SW First Ave Suite 1180 Portland OR 97201 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com Jaguar 5 5 User Manual 319 Chapter 15 Getting Help Generally e mail correspondence is best because you can send machine output if neces sary When sending e mail messages please include the following information most of which can be obtained by entering SCHRODINGER machid at a command prompt 320 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 Jaguar 5 5 User Manual References The first 18 references listed below provide general information about the algorithms used in Jaguar and some of their applications Their titles are included in the listings and copies of some of
508. ulations a These names are used in the grid related keywords described in Table 9 37 You can read in your own set of grid points and weights by using the gname 6 option and the GPTSFILE line of the input file which is described in Section 9 1 on page 161 Jaguar 5 5 User Manual 211 Chapter 9 The Jaguar Input File Table 9 37 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 for cal lcoarse culation 2 Basis functions are sorted into Imedium Ifine lufine lgrad short and long range gname gt 0 Specifies which parameter set from gcoarse 1 gmedium 2 grid file should be used for grid gfine 3 gufine 4 e g 2 for second ggrad 4 glmp2 4 glmp2der 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 none generated within Jaguar for grid listed by name 6 Use grid and weights from file none specified by GPTSFILE line in input file for grid listed by name dname gt 0 Specifies which dealiasing function dcoarse 1 dmedium 2 from the daf file should be used dfine 3 dufine 4 dgrad 5 9 5 24 Memory Use Keywords Some of the memory use for Jag
509. ule are listed The list ends with the number of exchange Hamiltonians 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 is a local MP2 calculation and you want to see the energy from each LMP2 pair use the gen section keyword setting ip170 2 as described in Section 9 5 19 on page 204 6 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 The information in the table includes whether a restricted configuration interaction RCI calculation including that pair will be performed Y or N for yes or no and what the configuration interaction CI coefficients are for the pair 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 h ig 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 electr
510. up 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 methylethylene H5 C CH CH 6 l f 12 oL oL 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 i 1 2 00 C in H2 C C or H2 C O 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 positive 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 nega tive number n the description 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 cor
511. urning this option on you can choose to print out information about the Gaussian functions that make up the basis set The functions in a basis set are made up of polyno mials of the appropriate degree multiplied by linear combinations of Gaussian primitives of the form ye 7 where N is a normalization constant and z is the exponent of the prim itive If the linear combination only includes 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 The output controlled by this option gives essentially the same information about the basis functions in two different tables after giving a list of atoms and the basis set used for each one The shell information table is printed first An example for a calculation of water with a 6 31G basis set is given below The first column of the table indicates which atom the 8 Keyword ip192 2 in gen section of input file 9 Keyword ip18 2 in gen section of input file 10 Keyword ip19 2 in gen section of input file 11 Keyword ip1 2 in gen section of input file 126 Jaguar 5 5 User Manual Chapter 6 Output shell is centered on The second column lists the shell numbers which increase consecu tively 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 descr
512. us step as initial guess for current geometry 1 For each step in a geometry scan generate the initial guess wave function according to the iguess setting nogas 0 For optimizations in solution perform gas phase geometry opti mization first to get accurate solvation energy 1 For optimizations in solution skip gas phase geometry optimiza tion and compute solvation energies using 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 optimiza tion and compute solvation energies using energy of initial struc ture as gas phase energy should yield same structure as nogas 0 intopt 0 Use Cartesian coordinates for optimization 1 Use internally generated 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 sec ond 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 Natom perturbed geometries by moving each atom pertnd bohr in positive or negative x y or z direction 2 Calculate frequencies numerically 180 Jaguar 5 5 User Manual Chapter 9 The Jaguar Input File
513. ustomizing Host Configurations eene Lateranen rect ettet 263 11 1 1 Themame and host Settings eee teet ren 265 1112 The user SOUS cmene e rero tte rei 265 11 1 3 The tempat x Setini uen vet E eee rro E E Ret hA Lippe d 265 11 1 4 The processors Seti iere ee Pepe treten enr 266 11 2 Th Saccus Command ere Remates 266 11 2 1 Selecting a Calculation Host ertt 269 11 2 2 Selecting Particular Jaguar Executables sess 269 11 2 3 Running a Jaguar Job From the Command Line 269 11 2 4 Kiling a Jaguar VODs iacet oreet de te gebe rap EUN 271 11 22 5 Converting Elle Formas ertet inrer bite rrt 272 11 3 Running Multiple Jobs jaguar bateh snc sii streets 275 11 3 1 Batch Input File Format tette nee 276 11 3 2 Batch Input File Exaitiple eee eter eet dees eene deer ete 279 11 3 3 Running Jaguar Datei etre rette ties ro EIER UR 279 Chapter 12 Troubleshooting e eee eere creen eene enean sense ene s tuse 281 12 1 Problems Gets Started i c roter e eripe rn eter s 281 12 1 1 The SCHRODINGER Environment Variable 281 12 1 2 Including the jaguar Command in Your Path 282 12 1 3 Problems Starting Massie ioco te teer teet idees ieri cessisse 283 12 1 4 Problems Related to Your Temporary Directory 284 12 1 5 Problems Running Jaguar Calculations
514. ut File Content for Calculation Options eene 106 63 J BEI ud east ees a sr E e escetae tees a E a 106 6 3 2 EMP2 iani e Re RRUME EE OR IRI SEI okey 106 oM oa E E A E E T A seats 107 6 3 4 GVB REI sinnir e aa ara tian aies pa aranhas 108 6 3 5 Geometry or Transition State Optimization HF GVB DFT and LMP2 109 6 3 6 Optimizations With GVB RCI Wavefunctions eeseeees 112 G37 NOL COD T 112 6 3 8 Geometry Optimization in Solution sese 116 6 3 0 JPEOBFUGS eet erroe dte co tsp e EH Ferre a e EIER 116 6 3 10 Frequency IR Intensity and Thermochemistry Output 121 6 3 1T Basis Sete rere ort Rr peii eet cete bee saath 123 ORB PAD RP 123 6 4 Standard Output OptiOns cerent ee eerte ree ree Ferte 124 6 5 File Quiput OBUOBS anderer ttt eter erre te ep et n e e RENEE 129 6 6 Output Options Per Iteration encinares a enean EEEN 131 6 7 Output Options for Orbitals eee alesis herb iere EEE 133 6 8 The Log File ar eerte ette rte dee eee Re per HERE HE E 136 Chapter 7 Tips and Suggestions e ceres eese eee ee eerte eese testen senos ena 139 7 1 Tips for Various Types of Jobs eerte terree 139 7 1 1 Organometallics and Other Difficult to Converge Systems 139 7 1 2 GVB Calculations GVB Pair Selection sees 141 71 5 Geometry ODUmILZaloll oe sen entrer ere ere e a e ere
515. ut file 16 Keyword ip163 2 in gen section of input file 17 Keyword ip175 2 in gen section of input file 130 Jaguar 5 5 User Manual Chapter 6 Output Molden orbitals file molf You can use this option to produce a file with the final orbitals in a format suitable for the program Molden 108 5 If you have run a frequency calculation the normal modes are written to the moLf file 6 6 Output Options Per Iteration Some output can be printed out every SCF iteration by choosing options from the Per Iter ation Output window which you open using the Per Iter button in the Output section of the Jaguar panel The output described in this section appears in the output file For each SCF iteration where the described output appears that output is listed before the usual energy data for that iteration Any non default settings from the Per Iteration Output window cause the output from the program pre to list the non default options chosen This output appears above the molec ular geometry output from the same program and indicates the keywords referred to in footnotes throughout this section energy components When this output option is off the individual components contributing to the total energy are only printed for the final converged result of the SCF iterations When the option is turned on the output includes each iteration s energy components namely the nuclear repulsion term the total one electron terms the total
516. ut files and results are in the same format as in the single initial geometry runs 318 Jaguar 5 5 User Manual Chapter 15 Getting Help For help installing and setting up licenses for Schr dinger software see the Schr dinger Product Installation Guide The Maestro help facility consists of Auto Help Balloon Help tooltips and online help To get help follow the steps below Check the Auto Help window located below the title bar of the main window If help is available for the task you are performing it is automatically displayed there If your question concerns an interface element e g a button or option menu there may be Balloon Help for the item Move the mouse pointer over the element If there is Balloon help for the element it appears within a few seconds If you do not find the help you need using the steps above click the Help button in the panel for whose settings you are seeking help The Help panel is opened and a relevant help topic is displayed For help with a concept or action not associated with a panel open the Help panel from the Help menu on the main menu bar or by using the key combination ALT4H If you do not find the information you need in the Maestro help system check the following sources The Maestro User Manual for questions about Maestro The NBO Manual for information about NBO calculations The Maestro Release Notes The Jaguar Release Notes The Frequently Asked Q
517. utomatically maxciit 32 Maximum number of iterations used for the diagonalization of the CI matrix 9 5 9 Geometry Optimization and Transition State Keywords Many of the keyword settings for optimization of minimum energy structures and transi tion states described in this subsection can be made from the GUI as described in Chapter 5 which also contains more details about the methods used for optimizations Table 9 17 contains optimization keywords that take on integer values Most default values for these 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 Jaguar 5 5 User Manual 179 Chapter 9 The Jaguar Input File Table 9 17 Integer Keywords for Geometry and Transition State Optimizations 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 iqst 0 Perform standard non QST transition state search 1 Use quadratic synchronous transit QST methods to guide tran sition state search Sets itrvec to 5 igscan 0 For geometry scans use converged wave function from previo
518. utput 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 Orbitals window as described in Section 6 7 on page 133 Jaguar 5 5 User Manual 123 Chapter 6 Output Standard Outp ut echo input file and parameter list memory disk and i o information El detailed timing information l geometries in atomic units also multipole moments in atomic units also d bond lengths and angles connectivity table geometry optimization details overlap matrix one electron Hamiltonian Gaussian function list basis set Gaussian function list derivatives Figure 6 1 The Standard Output window 6 4 Standard Output Options The menu options from the Standard output window are described in this section The output generated from these options appears in the output file for the job If you make a non default setting from the Standard output window the output from the program pre prints the non default options chosen This output appears above the molecular geometry output from the same program and indicates the non default values of the keywords referred to in footnotes throughout this section echo input file and parameter list If you turn this output option on the output from the program pre includes an echo of
519. v1 gconv7 sse 184 gdftcphf gdftder2 gdftfine gditarad 4 iei 210 253 gdftmed sss 210 253 geldens STI cos diete pb d d erit ns derad odd Ea e MER 212 dmedium 5o oro OE EREFUNGED I 212 QUfIne oiii e ha 212 epsout esolv0 esp extentx extenty extentz F fdtemp formal frag freqfrag Jaguar 5 5 User Manual MCAVICY zou dta eu RD OD n diia 187 jjj e 188 ichange sce AH et RS 196 ICIS 179 ICOV 4 uscacipivoo p REED DER EE RE 194 oj A 225 idelfrag 5 noii tete 226 Idelocy nicae i Reto 173 Idenavg 5 ice Rete 178 196 IdfgrdX acepte rore RR 210 iguess 198 199 227 igvball oe E eie 170 171 IgVbsel iiit fib inerte 170 171 345 Keyword Index Ihamtyp 5 199 230 iheter MINE VD o sit ce ue vit diets 170 199 ihuptyp iorb2a iorb2b iordboy ip1 ip3 ip8 ip11 ip13 ip18 ip19 ip24 ip26 ip170 ip173 ip192 ip193 204 205 1p100 scent HH PEE ine 209 ip100 101 ip103 107 209 ip105 sss 209 210 ip107 ip472 ip175 ilc RM iplotden 2 ets iplotesp iplotspn 2 oiii bcne ta ipltumnit iori or HPURON ORE ipolar ipopsym ipvirt IQCOATSE 1 iere 212 213 214 ilm 212 213 214 iqgrad
520. values whose mean ings are explained in Section 9 5 on page 168 At least one spacing character must precede and follow each keyword and each value For example Jaguar 5 5 User Manual 163 Chapter 9 The Jaguar Input File 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 keyword and its value must be on the same line Note that the following 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 9 2 The zmat zmat2 and zmat3 Sections The molecular geometry must be described in the zmat section Details on inputting a geometry through the GUI can be found in Section 3 2 on page 26 and Section 3 4 on page 34 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
521. w essere 56 57 gvbig program 107 232 GVB LMP2 calculations 57 58 GVB RCI calculations 56 57 153 155 H ham input file section 230 Hamiltonians information in output 104 107 108 131 user input of eese 230 harmonic frequencies 122 Hartree Fock HF calculations 56 102 103 105 137 keywords for SCF settings 193 196 output from standard 102 printing orbitals 133 135 200 used for GVB initial guess 76 108 heat capacity calculations see thermochemical properties Jaguar 5 5 User Manual Index Help p tiel tator nes 20 319 Help window sess 47 48 281 hess input file section eese 226 Io 3b NEP 85 92 coordinates for refinement of 32 effect of quality on geometry convergence 83 92 for IRC calculation 95 input file section 226 227 keywords for 181 183 level shifting 182 183 reading BIOGRAF in Maestro 35 refinement of initial 32 33 92 93 165 166 182 selecting initial 85 181 updating keyword for 182 Hessian refinement specifying coordinates TOW ss sts desta teed te acier editieren teta 93 heteroato
522. w Project directory vw Project jobs directory vy Other specify below Directory currentdir Figure 2 6 The Directory folder of the Preferences panel 1 Open the Preferences panel from the Maestro menu 2 Click the Directory tab 3 Select the option for the directory you want files to be read from and written to 2 12 Running and Monitoring Jobs While Jaguar jobs can be run from the command line we suggest that you use the Maestro GUI to set up and launch these jobs at least until you have some experience with the programs and understand the directory structure and the input file requirements Maestro has dedicated panels for preparing and submitting Jaguar jobs To use these panels choose Jaguar from the Applications menu Maestro also has a job control panel for monitoring the progress of jobs and for pausing resuming or killing jobs All jobs that belong to your userid can be displayed in the Monitor panel The text pane shows some kinds of output from the job that is being moni tored The Monitor panel opens automatically when you start a job If it is not open you can open it by choosing Monitor from the Applications menu in the Maestro main window You can monitor jobs from this panel whether or not they were started from Maestro When a job that is being monitored ends results from that job are automatically incorpo rated into the project If a job that is not currently being monitored ends you can select i
523. 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 solvation energy of a nonpolar solute of identical size and shape 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 functional 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 reorga nization 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 1 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 no
524. with the lowest energy The calculate forces only option computes the deriva tives of the energy for the input structure but does not change the geometry Another option is transition state search Settings specific to transition state optimizations are described in a later section of this chapter 5 1 1 Maximum Iterations An upper limit on the number of steps taken in the geometry optimization sequence can be set in the box marked Maximum iterations 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 Optimization settings described below 1 Keyword igeopt 0 in gen section of input file Keyword igeopt 1 in gen section of input file 3 Keyword igeopt 1 or keyword nmder 1 in gen section of input file depending on whether analytical or numerical forces are requested 4 Keyword igeopt 2 in gen section of input file 5 Keyword maxitg in gen section of input file Jaguar 5 5 User Manual 83 Chapter 5 Optimizations and Scans Geometry Optimization Maximum iterations 500 Convergence criteria default s Initial Hessian Schlegel guess d Trust radius n a W Fix
525. x accuracy prelim prelim update final final update gradient 35147 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 immedi ately 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 specified by the keywords gcoarse gmedium gfine gufine gcharge ggrad geldens gdftmed and gdftgrad Section 9 5 23 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 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 partic ular SCF
526. x in the z direction Only z should be nonzero ipltunit 0 Use atomic units bohr 1 Use angstrom units The settings for origin extentx extenty and extentz describe the box containing the grid points The edges of the box start at the origin and form vectors in the three directions determined by the coordinate values of extentx extenty and extentz whose three coordi nates should be separated by commas or spaces The number of points in each direction in the box is then given by npts another three dimensional setting The default units are atomic units bohr but you can change the default units to angstroms by setting ipltunit 1 Here is a sample plot section that generates plot information for orbitals 2 through 5 amp plot iorbla 2 iorb2a 5 npts 22 22 22 origin 3 150000 3 150000 3 150000 extentx 6 300000 0 000000 0 000000 extenty 0 000000 6 300000 0 000000 extentz 0 000000 0 000000 6 300000 amp Jaguar 5 5 User Manual 235 Chapter 9 The Jaguar Input File When the job is run each type of output requested by the plot section shows up in a file whose name depends on jobname the name for the job for example h20 for a job run from the input file h20 in and the type of information being plotted The file name is jobname density plt for a density plot or jobname potential plt fora potential plot Orbital plot information is written to separate files for each orbital whose names depend on the four digit orbit
527. y choose Save from the File menu to save your changes then choose Close from the File menu to close the Edit Geometry window To read in the structure click Read in the Jaguar panel 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 24 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Whichever method of entry you chose the molecular structure should now be shown in the Maestro main window If you entered the geometry by hand you must give the job a name by entering a single word in the Job Name text box in the Jaguar panel If you read in the sample input file the name H20 appears in this box The names of the input output and log files for your job depend on your entry the Jaguar input file is named jobname in the output file is named jobname out and the log file is named jobname 1og where jobname is your Job Name entry When you finish setting up your calculation click the Run button in the Jaguar panel The Jaguar Run window is displayed The calculation host the machine that the job will run on is listed at the top of the window If Jaguar is installed on more than one machine at your site you can change the choice of calculation host by selecting another name in the list The Temp directory selection is a directory on the calculation host that will be u
528. y clicking the Hide button If you want to reopen it later choose Monitor from the Applications menu in the Maestro main window Any additional jobs that you submit run concurrently If you exit Maestro any Jaguar jobs still running continue to run to comple tion For more information on the Monitor panel see Section 3 9 1 on page 46 or see the Maestro User Manual 3 6 Running Batch Jobs or Scripts You can run multiple Jaguar calculations in a single run using the Jaguar Batch window which you open using the Batch button in the Jobs section of the Jaguar panel For instance you can run 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 40 Jaguar 5 5 User Manual Chapter 3 Running Jaguar From Maestro Jaguar Batch Script Use existing script Name BUILTIN SCRIPTS TOBS Varta Script This script requires input structures for processing Inputs Use selected disk files af Select input files Hamme i Virite Input File 1 input file has been selected Job Host localhost epus 1 Tapie iset 2a Job Dir zone1 juliem jaguartest RUN Cancel Help Figure 3 7 The Jaguar Batch window Several Jaguar batch scripts are included with the program You can also write your own batch scripts or save job setup in the Jaguar Batch window as a batch script Section
529. y 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 molec ular 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 covalent 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 shell 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 ea
530. y its formal charge in the atomic section see Section 9 8 on page 218 Also if the geometry files are not in Jaguar format you can translate them using the Read and Save windows see Section 3 4 and Section 3 7 or Babel see Section 11 2 5 on page 272 or type jaguar babel in a terminal window for usage instructions The acidic site can be marked using one of the following methods By adding the suffix _pk to the atomic symbol By setting the amp gen section keyword ipkat to either the atom s name or to the atom s order number in the amp zmat section If you make this setting in the Edit Input panel in Maestro you must save the input file to disk before starting the pK job Here are three equivalent input file examples for formic acid amp zmat cil 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H pk 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp zmat ci 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 Jaguar 5 5 User Manual 315 Chapter 14 The pKa Prediction Module amp gen ipkat H1 amp amp zmat CI 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 348981310
531. y window The main geometry needs no special options To build Geometry 2 or Geometry 3 in the Workspace click Structure in the Jaguar panel then select Geometry 2 or Geometry 3 from the Displayed Structure menu The Work space is cleared and you can now build the structure To read in a geometry as Geometry 2 or Geometry 3 set the Read as option in the Read window to Geometry 2 or Geometry 3 To create or edit one of these geometries in the Edit Geometry window choose Geometry 2 or Geometry 3 from the Structure menu If you want to use the same Z matrix for Geom etry 2 or Geometry 3 as you are using for the main geometry choose Use initial geometry Z matrix from the Z matrix menu You can then set the variables to the desired values 5 3 3 Initial LST Guess If you provide reactant and product geometries for a QS T guided search but do not provide a transition state guess Jaguar generates a transition state guess by interpolating between these two structures 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 to the reactant geom etry 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 22 zmat2 section of input file 23
532. yn wos scic ccdi cessieets enea A ERE ENEE 304 14 3 3 Multiple Protonation Sites rentrer ipei 305 14 4 Framing Set Results ettet eret mre PE REPRE SES 305 14 5 Running pK Calculations 2 m ertet 315 145 1 Activating the pKa Module tette 315 14 5 2 Jaguar Input Files for pKa Calculations eese 315 14 5 3 Ruunmg pKa Calculations eerie eei tee nitet 316 14 5 4 Monitoring pKa Calculations eoe ette 317 14 5 5 Initia Geometry 1er rrr rm tr err ede ripe re ipea 318 Chapter 15 Getting Help ccsccccscccescoacsoessessesosessssessesssvossssonssoossoossessoessoesseosesss 319 is lo po M RA 321 Di f 329 Keyword TAG OR qe rsss 345 X Jaguar 5 5 User Manual Chapter 1 Introduction 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 graphical user interface GUI Online help is available in the GUI although the information in this manual is generally more comprehensive The GUI for Jaguar is part of the Maestro GUI Chapter 2 introduces the main features of Maestro and provides instructions for setting up your environment and running Maestro Chapter 3 contains information you will need to run Jaguar including information about using the GUI geometry input formats specify
533. ype 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 irrele vant However keep in mind that the order of the atom type descriptions is important since the first matching description will always be used 258 Jaguar 5 5 User Manual Chapter 10 Other Jaguar Files 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 characteris tics in turn Atomic number for instance 6 for carbon Hybridization of the atom itself 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 electrons where n is a non negative integer 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 indi cating that any value for that characteristic matches that atom type description
534. zation 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 Final pK and pK values are calculated from data in these output files and written in jobname out in the local directory where jobname in is a Jaguar input file submitted for a pK calculation For example here is the final output file for formic acid Stoichiometry Charge pK CH202 0 pKa 3 2 CHO2 1 pKb 10 8 To list in a table all the pK and or pK values you can use the jaguar results command jaguar results title jobname pka pkb out Jaguar 5 5 User Manual 317 Chapter 14 The pKa Prediction Module 14 5 5 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 to determine the global minimum energy structure which can then be used as an initial struc ture for the pK run For certain systems it is expected that the protonated and deprotonated structure assume different conformations in their lowest energy state For such cases create Jaguar input files for both of them and use the deprot option of the jaguar pka command to specify the deprotonated structure Outp
535. zepin 2 one 4 0 3 5 0 5 2 3 dihydro 1 methyl 5 phenyl 1 4 benzodiazepine 6 2 6 2 0 0 3 hydro 2 methylamine 4 oxy 5 phenyl 1 4 benzo 3 2 4 8 1 6 diazepine GUANIDINES clonidine 7 8 8 1 0 3 debrisoquin 12 0 11 9 0 1 guanidine 12 4 13 8 1 4 methylguanidine 13 2 13 4 0 2 PYRROLES C 2 protonation pyrrole 2 9 3 8 0 9 methylpyrrole 22 2 9 0 7 2 methylpyrrole 0 7 0 2 0 5 3 methylpyrrole 0 8 1 0 0 2 INDOLES C 3 protonation indole 3 7 3 6 0 1 methylindole 2 1 2 3 0 2 2 methylindole 0 5 0 3 0 2 3 methylindole 4 7 4 6 0 1 314 Jaguar 5 5 User Manual Chapter 14 The pKa Prediction Module 14 5 Running pK Calculations 14 5 1 Activating the pKa Module To run the pKa module you need a special license in addition to the regular Jaguar license To install the pKa module first install Jaguar using the instructions in the Schr dinger Product Installation Guide After you have successfully installed Jaguar send in the machid information to obtain a license to activate the pK module Explicitly indicate in your license request that you want to run pK calculations 14 5 2 Jaguar Input Files for pK Calculations pK calculations require input files in Jaguar format containing a molecular geometry and a labeled acidic site The acidic site is either an acidic hydrogen in acids or a heteroatom to be protonated in bases If the starting geometry is not a neutral molecule but an ion you have to specif
536. zvar section amp zvar ycoorz0 753108 zcoorz0 454006 amp For an optimization to constrain freeze all bond lengths or angles set to a particular vari able 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 7531084 zcoorz0 454006 amp would if used in an optimization freeze all ycoor values to be equal to 0 753108 during the job Certain types of transition state optimizations require that you enter two or three geome tries see Section 5 3 on page 88 for details For these jobs you can specify 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 9 4 The coord and connect Sections For some geometry or transition state optimizations you might want to specify that the optimizer 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 coordinates

Jaguar 5.5 - Stuchebrukhov Group

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