Home

TmoleX User Guide

1. 3 as usual a right mouse menu is available Simply select one or several lines in the tables and click on the right mouse button Choose Molecular Orbital s Lee g ee a o e ee NNNNNOG OESOO F Choose Density and Electrostatic Properties Sel Plot propertyname Ground state total density ist derivative of total density 2nd derivative of total density Laplacian of total density Kinetic energy density Electrostatic potential Electric field Gradient of electric field Electrostatic potential color coded on density isos des r er er er er er er a e e er er ar er es ae Page 57 92 3 The 3D visualization If you choose several options like orbitals densities electrostatic potential etc each property will have its own progress bar All properties which require solving integrals like electrostatic properties densities and their derivatives are quite expensive Especially for larger molecules generating 3D plot files can take much longer than the single point calculation or a geometry optimization When the calculation is finished the orbitals or properties can be selected for visualization Several properties can be displayed in the same window Check the memory usage of TmoleX from time to time when using this option Just click directly on the buttons which have now a green check to show that 3D data is already available for vis
2. Run network The job can either be started on the local system or submitted to a remote machine using the Run network button While the job is running the icons in the job tree will change The job status during the run can also be displayed and visualized Here the first job a geometry optimization is running The status of this job is therefore printed as Energy vs the geometry cycle Page 72 92 6 Job Templates File Edit Templates Results Extras Tools Help 5 D 525 E 6 P open 3D Mokcular Builder v E ProjectList E TmolexProject Y job_GEO_1 Y job_GEO_5 Y job_SP_6 Y job_SP_7 Y job_SP_8 v 7 job_SCAN_9 Y scan_0000 Y scan_0001 Y scan_0002 Y scan_0003 Y scan_0004 Y scan_0005 Y scan_0006 v 7 job_SCAN_11 Y scan_0000 Y scan_0001 Y scan_0002 Y scan_0003 Y scan_0004 Y scan_0005 Y scan_0006 Y scan_0007 RE J scan_0008 job no 0 is currently running H Y scan_0009 ENERGY Memory used for Tmokx __176 8 275 6 MB System Molecular Attributes gt v Apply Job Template Jobs running local 1 4 remote 0 500 0 6296 2 MB x Charge Atomic Attributes Results OPT FREQ xml Name job_GEO_1 job_GEO_5 job_SP_6 job_SP_7 job_SP_8 job_SCAN_9 job_SCAN_11 job_TEMPLATE_14 Start Jun 2 2014 4 06 53 PM Jun 3 2014 9 47 47 PM Jun 4 2014 9 59 40 AM Jun 4 2014 10 21 54 AM Jun 4 2014 10 26 40 AM Jun 4 2014 10 38 31 AM Jun 4 2014 10
3. 7 Batch processing 7 Batch processing The job templates described in the previous chapter can easily be applied to any kind of structure the user does not have to take care of anything else but to read in the coordinates or build a molecule set the charge or accept the defaults apply the template and start the job To open a new batch job just use the File New Batch Job entry in the menu or click on the lb button in the tool bar TmoleX will generate a new job the geometry menu of this job is shown 4 TmoleX 4 0 TmoleXProject x Fie Edit Templates Results Extras Tools Help gt is H w Y Jobs running local 0 4 remote 0 Memory used for Tmolex 154 2 270 2 MB System 0 0 6296 2 MB v E ProjectList lt gt p _ gt Y 5 TmolexProject AAA a gt Y job_GEO_1 Choose Job Template Charge Apply Job Template Y job_GEO_5 Y job_SP_6 Coords Sym Multiple Coordinates Y job_SP_7 ro Y job_SP_8 e Add Molecule Delete Molecule gt 3 job_SCAN_9 gt job_SCAN_11 gt job_TEMPLATE_14 job_notRun_15 Number Name Charge Image click to view modify Apply Job Template amp Prepare to Run Manage Job s 7 1 Read in and use several molecules Batch jobs apply predefined job templates to a list of molecules The molecules have to be read in from file by using the 2 add Molecule button This opens a file browser which also allows to read in file fo
4. Generate batch jobs from existing jobs Another possibility to generate a new batch job and to read in structures is to select a list of finished jobs in your project and job tree and click on the right mouse button Y E ProjectList Y 5 TmolexProject j job_GEO_1 job_GEO_5 Y ENE Job Results Scan jo sf job_SP_7 A Y job_SP_8 Type of Calculation Sin Y job_SCAN_9 x scan_0000 Y dscan_0001 x scan_0002 2 scan_0003 Energy o oO o an oong ven cir VIBRATION 2 scan_00 Export Results 2 scan_00l Kc 410010 ea 90 gt o job_SCAN_ Y job_TEMPLATE_14 job_0000 Y djob_0001 v ll job_BATC y ES Vibrational Modes 2 propylamine s aniline 24 a 10 7 a 11 Page 77 92 7 Batch processing 7 2 Apply templates for batch jobs Once you have a complete list of molecules to perform calculations on select a job template from the tool bar Important The charge field can either have numeric entries which will assign the given charge to all molecules or it can be empty in this case the charges that are displayed in the table will be used The default which applies when no charge is imported from the coordinate files is zero Geometry El gt gt GEO OPT guick xml Apply Job Template All settings for basis set method job type etc can not be changed in batch jobs since they are defined in the job templat
5. AM1 PM3 MNDO MNDO 3 are the available methods they all are parametrized for a certain number of elements AM1 COSMO is the default setting for COSMOtherm input files at BP SVP level first do a geometry optimization at this level and then a single point DFT calculation with COSMO and SVP basis set Unrestricted calculations can be done with UHF guess structures for transition states can also be searched A molecular charge has to be entered to calculate ions Page 46 92 3 The 3D visualization 3 9 Labels and Measurements Labels for atoms and bonds as well as measures of lengths and angles can be switched on or off for the complete structure or individually for each object e Display labels for all atoms or bonds In the 3D viewer select Tools Visual settings and switch to the Labels section Viewer options COSMO cavities Properties General Molecule Load Defaults For atoms the atom number the element symbol the charge and additional text which can be entered by the user with the right mouse button menu within the viewer window can be displayed Depending on the background colour and the colour of bonds and atoms the labels can be hard to read The background settings here refer to the background of the text field only Page 47 92 3 The 3D visualization e To display labels of one or several atoms bonds only use the right mouse menu Own text can be entered in the second item of the
6. Machine P Group Name User Work directory TURBOMOLE direc UseCPU Utilized CPUs RAM MB Queue Y SGE duster gt enzo4aduster duster SGE duster 394 scrfm394 fusr app TURBO 41 0 0 va aaa tmolex linux 14 linux14 Default tmolex homeftmol software TURBO 1 o o G a tndlex 10 0 0 ILLES Default tmolex home tmol software TURBO 1 0 o un J tmolex 10 0 0 208 PPP a Copy Machine Delete Machine Export Machine Import Machine To see how many jobs are already running on the remote system use the right mouse button menu and click on Check workload This will call top on the remote system and show the results Page 81 92 7 Batch processing current 5 min average 15 min average 0 01 0 05 0 08 F Show expert information top 12 38 00 up 494 gale 22 46 7 users load average 0 01 0 05 0 06 Tasks 189 total 1 running 188 sleeping O stopped O zombie Cpu s 13 7 us 0 6isy 0 8 ni 84 63id 0 23wa 0 03hi 0 0 si 0 0 st Mem 32207M total 31964M used 243M free 261M buffers Swap 65538M total 662M used 64676M free 29219M cached PID USER NI VIRT RES SHR 10540 0 CPU MEM TIME COMMAND 0 a S227 571 EE 0 05 61 kthreadd 5 1 root 5 S 5 35 03 ksoftirad 0 5 S 5 root root 12 44 06 migration 0 1 39 27 watchdog 0 14 52 08 migration 1 root I 0 0 root 0 0 0 0 root In the first line the load i e the number of running time consum
7. Single Point Properties gt Potential Energy Scan PES P Templates gt Batch processing gt This opens a new option section for the job Select singlet or triplet either full RPA TDDFT or using the Tamm Dancoff TDA approximation the number of excitations and run it Excited states Singlet _ Triplet RPA Random Phase Approx y RPA Random Phase Approx Unrestricted No of excitations 5 TDA Tamm Dancoff Approx Unit nm w The spectra can be opened with the CD or UV Vis Spectrum button Open Files Output Energy Moments ts UV Vis Spectrum tes CD Spectrum ps Raman Spectrum pa IR Spectrum Page 65 92 5 Constrained optimization and Scan jobs 5 Constrained optimization and Scan jobs 5 1 Defining fixed internal coordinates TmoleX allows to define internal coordinates Bonds bond angles and torsions can be fixed within the builder To define a constraint select one two or three bonds e select one bond click on the right mouse and choose Scan freeze length Am0 Bond Atom Style Label Edit additional label Measure torsion Scan freeze length Guess length Guess dihedral angle Change torsion Add atom at center Delete On the right the options for freezing a bond length are show To delete constraints select here and Objects Constraint stre C8 C9 v delete Constraints Constraint stre C8 C9 Y Delete ne
8. 3 6 3 Change torsion To change the dihedral angle click on the middle bond or select three bonds holding shift key will add selections which define the angle and then either use the button on the left that will show up or again the right mouse menu Ly LJ TmoleXProject job_notRun_3 a Bond Atom Style Label Edit additional label Measure torsion Scan freeze length Scan freeze torsion Guess length Guess dihedral angle Change torsion x Add atom at center Delete The torsion around which the molecule will be rotated is being shown Use the left mouse button to change the angle moving to right or up will increase the value moving the mouse to the left or down will decrease the angle The value of the angle can be entered directly on the right side and one can also choose if the smaller or the bigger fragment is being moved TmoleXProject job_notRun_3 x Number of atoms 9 Number of bonds 8 Objects lt muttiple selected gt Angle 115 14 O smal fragment big fragment Page 42 92 3 The 3D visualization 3 Change bond angle To change a bond angle select two adjacent bonds shift click for the second one and either click on the button on the left side or use the right mouse button to change the value In E Z 9 te TmoleXProject job_notRun_3 x Number of atoms 9 Number of bonds 8 Objects l
9. selected will be by default the centre of the rotation Use the right mouse menu or the button O or the key e to switch to rotation mode k TmoleXProject job_notRun_13 A RO OSA Nix Rotation of the selected atoms can be done using x y z axis as rotation axis In addition to that the yellow circle indicates the rotation around the axis that is perpendicular to your screen at the moment you activate the rotation mode Use the right mouse button to rotate the view the middle Page 50 92 3 The 3D visualization mouse button to move the camera and the scroll wheel for Zoom Those mouse movements will not change the coordinates just the view To rotate around x y Z or the initial view direction use the left mouse button and drag the mouse Rotate tool x Pivot x 1 95 y Pivot Y 0 758 Z n Pivot Z 0 67 View n Around View Pivot at COM x Y View Use the coloured buttons on the right side of the window to switch the rotation axis or click directly on the coloured circles The around view button will reset the yellow view rotation axis to your current viewing direction Note that rotating the view with the right mouse button does not change the rotation axis The Pivot at COM changes the centre of the rotation to the centre of mass of the selected atoms Rotation angles can be entered in degrees to the corresponding X Z Y View fields The center of rotation i e the pivot
10. COSMOlogic Predicting Solutions Tmolex A Graphical User Interface to the TURBOMOLE Quantum Chemistry Program Package User manual COSMOlogic GmbH amp Co KG Imbacher Weg 46 51379 Leverkusen Germany Phone 49 2171 363 668 Fax 49 2171 731 689 E mail turbomole cosmologic de Web http www cosmologic de Version 4 1 June 2015 Page 2 92 Table of contents A N smeaee wanee cama aecee aetna sacaenmea ce eeee 5 MALAISIA A asa snes ene eee 5 LE AAA o PX eee ee ee 6 To MIC OSiR T 14 Online Updates iii A E 8 A e E O II cided kee es eRe lesa teal aclad anata pale cae Noha 9 Z ls Stare Ne Proa Mini A o 9 2 2 AN MUS trate xamples Fant Tenani dd iR 11 e o PP A A 12 ZA VINE SECOS o td Al aoe 13 ZS AR Mus trative example Farn Zo dd did 15 20 Geometry panel eS tee 15 292 BaSS A aerated gels a aus tac beacesecewnv eevee elle te 16 2 0 9 Molecular Start OrpitalS Da elias A ee Adee 18 25 4 Level of theory Select MONO ii A A A A A ore 20 2 5 5 Start Job Select kind of job and Start it cooonccccononoconncoconononanononcnnoconcnononononannnonnnnnonannnnnananons 22 A co E acted re tang ud pce cade EN 24 26O JOD AdMINIS TAUNO ees a A iio 25 SEDA o A A a 27 A A a E A 27 ERNA Lo E LL e O a a A tava keene 28 iZ Restore GS TUCU Ss a ai cicia 29 S2 POS MUC IUE ee ee eee en ee eee Sore ee tee eee EN 30 59 gt USE SMILES COG a ee 31 3A Pe ZO A a enuns E 32 0 EASY DUNNING Faint ioo asese 33 3 6
11. E Add new Machine yg Save Machine yg Save Machine as El Import Machine Et Export Machine Note runs only on Linux Unix systems a y Remote machines 4 Y Default b Machine IP Clear Add New _ user machine User Copy Machine Password Import Machine Group name Default AE Identification yserfimachine Delete Machine Work directory TURBOMOLE directory Number of CPUs for job s Check remote system every 1 min TURBOMOLE version unkown number of CPUs in use __ Use queuing system General informations about a remote system are 1 The name or the IP address of a remote machine Machine IP field 2 User name on that machine 3 Password to log in Page 85 92 8 Remote jobs Those three fields have to be filled in first To check if the settings are correct and if a connection can be established click on Check Password Settings TmoleX will try to log in and determine the home directory of the user which has been given in the User field If the connection has been successful the home directory will be added to the Work Directory field 4 Work directory tells TmoleX in which path on the remote machine the job shall run a fast local disk should be chosen here 5 TURBOMOLE directory has to be set to the TURBOMOLE installation directory on the target system The default behaviour of ssh when starting remote jobs without an
12. This will result in a 2D surface which represents the iso value of the density and the colour on the surface is given by the value of the chosen property at that points Typical example open electrostatic potential use the isoplot option choose td plt for the total density and set an iso value This will give a typical picture of a electrostatic potential on an density isosurface lsosurface plots two iso densities one at the positive value and one at the negative value A typical molecular orbital picture Page 59 92 3 The 3D visualization Vector plots Vector fields can be visualized too the best way to get an idea of the field depends on the property Most options are similar to those described above Objects lt nothing selected gt M Page 60 92 4 Properties 4 Properties 4 1 Vibrational frequencies If you have an optimized geometry you might want to follow it up by a frequency calculation either in order to check if you are in minimum or because you are interested in the IR spectrum File Edit Templates Results Extras Tools Help 13525 E 65 9 oven 30 molecular Builder v fi Projecttist ce Atomic Attributes olecular Attrib Mel y E TmolexProject A A A a A o job_GEO_1 Charge Use from input w Apply Job Template Y job_sP_2 job_SP_6 a X X X X X X XX Geometry Optimization Ground state Level DFT Disp Functional pbe Spectra
13. can also be entered manually if needed Note that the selected atoms which will be rotated do not have to be connected e Moving atoms or fragments is very similar to the rotation procedure described above Select the atoms that shall be moved and use the right mouse menu Translate or the button O or press the key w Hints Double click on an atom to select the whole fragment all atoms that are connected by bonds o There is an option Select bond partners in the right mouse menu which extends the selection around each already selected atom to its next bonded neighbours Page 51 92 3 The 3D visualization File View Edit Tools Display Type Window Help a a a 2 O Q a Gradients Vib Modes J Internal Coords Builder Orbital Viewer TmoleXProject job_notRun_4 x f Number of atoms 12 Number of bonds 10 Objects _ lt multiple selected gt l A o a Translate tool gt Ay carbonyis gt dy hydrocarbons gt Wy misc gt de pah gt Wy rings Y 6 smal_common ch4 sdf Ml h20 sdf h2s sdf hen sdf nh3 sdf nitro sdf 300000 p left mouse button Click a handle and drag to translate the selection right mouse button rotate MMB move wheel zoom Again change the direction of movement either by clicking on the coloured buttons on the right side or by clicking on the coloured arrows Note Holding the left mouse
14. lt and gt go stepwise back and forth It is also possible to click on one of the circle in the graphics on the right which plots the total energy vs the geometry cycle The Calculate bonds check can be set to re check the bonds with respect to the atom distances in each step Page 54 92 3 The 3D visualization 3 12 Surface plots Once you have converged molecular orbitals TURBOMOLE offers the possibility to write different properties on a grid for a visual post processing This is reproduced in TmoleX interactively starting from Orbital Density Plot File Edit Templates Results Extras Tools Help gt fo cow E gt 9 Open 30 Molecular Builder v iH Projecttist Y E TmoleXProject Y job_GEO_1 Choose Job Template Y o Charge Use from input w Apply Job Template Y job_sP_2 Y job_SP_3 Type of Calculation Geometry Optimization Converged SCF Convergence Open Viewer 3 875 ev Orbital Density Plot Status geometry Converged Convergence Gradients Geometry Convergence Criteria Sconvinfo energy change actual value 0 000 threshold 0 1000E 05 geom gradient actual value 0 3718E 04 threshold 0 1000E 02 Open Files AR ee E eee Output kinetic energy 1149 72993725945 potential energy 2307 90686762554 a A Moments 1158 17693036609 a a a 3 a SCF energy 1158 1693245640 dE dxyz 0 043440 SCF energy 1158 1697110240 dE dxyz 0 0
15. 20 92 2 A quick tour Settings for SCF convergence and special COSMO selections recommended only for expert users can also be found in the method section Atomic Attributes Molecular Geometry Choose Job Template Charge Level of Theory Q SCF Convergence SCF convergence pani Energy convergence 10 Esa Density convergence Example 1 0d 8 Max number of SCF iterations 39 DIS damping Start 0 700 Min last 9 100 step 0 050 Energy and or density convergence criteria can be entered in this panel A density convergence criteria is useful for properties and methods that need a very accurate density like post Hatree Fock methods or TDDFT Note that the format of the parameters is different The exponent has to be entered for the energy convergence while the density convergence threshold is a total number like 1d 8 use d instead of e like 1e 8 because T URBOMOLE reads them in as double precision number This difference is due to the fact that the two corresponding TURBOMOLE keywords scfconv and denconv in the control file are have to be given exactly like this so TmoleX here tries to help to understand the default TURBOMOLE input Changing the default DIIS damping settings might be needed for complicated electronic structures like transition metal compounds If the energy does not converge within many SCF iterations the DIIS damping factors should be incre
16. 84369068 182 38424399 188 45435446 2c 63 84994381 182 39904285 188 57243313 Bu 3 c 1 63 84084530 182 38270866 188 45481295 4 c 1 63 84586533 182 38520047 188 45188219 Es 5 c 1 63 85164377 182 40001089 188 57046808 les 6 c 1 63 84042696 182 38267219 188 45529017 a 7h 1 2455004417 5 53087549 5 08872411 E 8 h 1 2456448603 5 48342201 5 04958979 9h 1 2455141466 5 53295887 5 08218234 aa 10 h 1 24 55027160 5 53118500 5 08910415 e 11 h 1 2456467651 5 48368315 5 04989062 saa z 12 h 1 2455138400 5 53289760 5 08211459 Era ohik caet data asop end Save as job template for further usag lt lt Previous Manage Job s Copy and paste the values to a spread sheet for further usage Note that to get the NMR ifts you have to do a calculation also on the reference molecule like TMS for carbon with the same method and basis set The NMR shieldings can also be displayed as labels in the viewer click on NMR Shieldings to open this view Page 64 92 4 Properties 4 4 UV Vis and CD spectra TD DFT A TD DFT calculation is set up like a normal DFT calculation Then choose Excited States in the job selection Geometry Optimization P Spectra amp Excited States FIR amp vibrational frequencies Single Point P ROVNE RS n ce E citations NMR shieldings Raman amp vibrational frequencies Optical rotations dynamic polarizability Transition State Search P Static polarizability
17. THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE e PuTTY uses its own repository for public ssh keys so ssh connections that do not require a password on your local machine at the command line might not work if OpenSSH or any other ssh program is used Run ssh from the TmoleX directory to check that manually e jobs can be killed while they run on a remote system For that purpose a kill job script is being stored in the directory where the job is running This script does kill all processes that are running in the directory the script itself is located but this will only work on systems where a proc directory is present usually all Linux systems and most Unix systems either e Passwords entered in the password field will not be saved to disk Hence they have to be entered each time TmoleX has been started but kept in memory as long as TmoleX runs Page 84 92 8 Remote jobs 8 2 Add new remote machine When starting a remote job for the first time or when you want to add several external machines several things have to be set TmoleX needs to know in order to be able to run TURBOMOLE there To start a job on a remote machine or to set or change settings click on Run network in the Start Job panel Save and Run Run local Save Run network TmoleX will first save the input file to a local disk under the usual naming scheme and then open a new window that looks like this one
18. amp Excited States PB MPAA Single Point gt UV Vis and cos tical excitations aie Basis set def2 SVP Single Point Properties gt Convergence Parameter Potential Energy Scan PES Optical rotations dynamic polarizability Eneray 6 Static polarizability 10 Transition State Search gt Templates gt Batch processing gt Use resources Memory used for 1000 0 Options Disk A Convergence criteria E Energy 6 101 Hartree Gradient norm 3 dE dxyz 101 Hartree Bohr F Delete scratch files after run Max no of cydes 50 Use internal redundant coordinates Save and Run Choose IR amp vibrational frequencies in the Start Job panel and click on Run In addition to analytic 2 derivatives TURBOMOLE is also able to perform 2 numerical derivatives for all properties which have an analytic gradient implemented For post Hartree Fock calculations or if COSMO is switched on the numerical option is chosen by default NOTE 2 numerical derivatives can not be performed with the Windows version of TmoleX Please submit such jobs to remote Linux systems Page 61 92 4 Properties To visualize the vibrational frequencies and or to distort the structure along a vibrational mode start the 3D Viewer by clicking on the Vibrations button Fle Edit Templates Results Ex
19. button to set a freezing point for frozen core approximation settings and the right mouse button to zoom in or click once to zoom out Page 19 92 2 A quick tour 2 5 4 Level of theory Select method In the Method panel you can choose the level of theory activate COSMO select auxiliary basis sets and advanced SCF settings can be changed File Edit Templates Results Extras Tools Help i Db da Co Dl 9 Open 3D Molecular Builder Jobs running local 0 8 remote o System 0 0 17087 9 MB Y Il Projectiist Goon Atomic Attributes lt Molecular Attributes Method Stat Job __ Y G TmoleXProject b B job_notRun_1 Choose Job Template Y a Charge Use from input w Apply Job Template Level of Theory pF Convergence Solvation Auxiliary basis sets for RI J Element Basis set Auxiliary basis set DFT settings c def SV P def sv p H def Sv P ws P def sv P Gridsize m3 DFT COSMO _ Activate F Two component treatment The level of theory for your calculation can be set here Currently nine different methods are available within Tmolex e Hartree Fock e DFT with or without RI J RI DFT is the default if you start a new session of TmoleX e DFT Disp DFT with empirical dispersion correction with or without RI J e MP2 e CC2 e CCSD e CCSD T Spin scaled SCS SOS MP2 or CC2 calculation can also be used as sub options to the MP2 and CC2 level Page
20. explicit shell or terminal is such that not all settings on the remote system are sourced So it is very likely that your TURBOMOLE settings like TURBODIR PATH etc are not available in such a case It is therefore unavoidable to set the PATH to the TURBOMOLE directory on the remote system by hand 6 The number of CPUs can be left unchanged Note that this field is not to tell TmoleX how many CPUs or cores are available in general but how many CPUs shall be used for the calculation of each job 7 Note that all jobs are started on the remote system with nohup TmoleX does not get a notice when the job has finished so it has to check actively whether the job is still running or not The frequency for those checks can be given in minutes 8 The TursomoLe version on the remote machine is needed to determine which program is used for post Hartree Fock calculations Since version 7 0 CCSD and CCSD T jobs are done by the program ccsdf12 and not by ricc2 any more as it was in previous versions 9 The queueing system option can be used to submit remote jobs to a queue which is accessible on the remote machine After settings 1 5 are complete click on 7 save Machine The Identification is used as name in the list of known remote systems given in the tree on the left side of the window Configuring a remote system such that number crunching programs like TURBOMOLE can utilize the hardware resources correctly is not a trivial tas
21. initial molecular orbital are displayed Page 18 92 2 A quick tour File Edit Templates Results Extras Tools Help k E s 25 ES E 5 9 oen 3D Molecular Builder Jobs running local v Projectiist Y 5 TmoleXProject Choose Job Template Y _ Charge Use from input w Apply Job Template Molecular Orbitals Molecular Orbitals Molecular charge 9 7 m 4 Energy Hartree Multiplicity 0 4338 0 4338 restricted Fully occupied 24 0 4819 0 4819 Partly occupied 0 0 5090 0 5204 0 5204 0 5655 0 5835 0 6165 Generate MOs Advanced settings Fermi settings Fermi Frozen orbitals for MP2 CC Freezing point Hartree te tetretrrrrrrr ttre AAA P wee PT PRR RP EB HE B 2 N Who DN OO amp The default for the multiplicity is automatic TmoleX will generate molecular orbitals by doing an Extended Huckel Guess and fills in the electrons according to the orbital energies It will recognize closed and open shell cases and switches to restricted RHF or unrestricted UHF settings Note that you have to generate new orbitals if you change the multiplicity In this case i e multiplicity not set to automatic will always result in unrestricted calculations In this panel you can also freeze core orbitals for correlated calculations or switch on Fermi smearing Switch from Table to Diagram to see the orbital occupation graphics Use the left mouse
22. t borazine sdf P imidazole sdf id indole sdf l pyrazole sdf pyrrole sdf pyrrolidine sdf E thiophene sdf File Name benzene sdf Files of Type all coordinate files Option 1 Read in a coordinate containing file The buttons Y a pa a oP siggy Import Coordinate Hie in the tool bar and the main window or the menu Import Coordinate File in the pull down menu File will open a file browser Select the coordinate file and load the molecular structure of benzene into TmoleX first change to your home directory and from there to COSMOlogic AppData TmoleX15 fragments rings Option 2 click on Open 3D Molecular Builder and double click on the benzene entry on the right side which is also located in the rings section Molecules Atoms MISC i pah Y 4 rings IM benzene sdf q lt benzimidazole sdf borazine sdf Page 11 92 2 A quick tour 2 3 The tool bar la a H y P Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 56 7 115 0 MB System 0 0 6296 2 MB The tools in the tool bar act only on the job that you are currently working on e which is opened in the project list F Create new job within the current project Create new batch job within the current project Lr 1 Read or import coordinates besides TURBOMOLE also many different formats E Yi 1
23. 0 Transition State Search gt A Caution constraint geometry Templates gt You have fixed internal coordinates Batch processing gt Use resources Options Memory used for 500 0 MB Convergence criteria Disk 0 MB for HF Energy 6 10 Hartree No of CPUs 1 ee 3 dE dxyz 10 Hartree Bohr Delete scratch files after run Max no of cycles 50 14 Use internal redundant coordinates Save and Run Run local Save Run network lt lt Previous Manage Job s If you have frozen bonds angles or torsions make sure to use internal redundant coordinates otherwise your settings will be ignored As long as you have constraints defined it is not possible to run an optimization without internal coordinates Constrains are always applied in this section no matter if ground or excited states calculations are done minimum search geometry optimization potential energy scans or transition state searches are started Page 68 92 5 2 Use internal coordinates 5 4 Scan along an internal coordinate The potential energy scan PES method can be applied if internal coordinates are defined and at least one of them is defined as fixed Scan will run a couple of geometry optimizations for a range of values of an internal coordinate Note that all fixed internal coordinates will be kept fixed not just the one that you have defined to be scanned along For a one dimensional scan job only one internal coordinate should be de
24. 1 1 Navigation Left mouse button or L or q on the keyboard Select Right mouse button or Rotate view Middle mouse button or a Move Scroll wheel or al Zoom Orbital Viewer B benzene sdf benzimidazole sdf borazine sdf P i left mouse button Click or drag to select right mouse button rotate MMB move wheel zoom Page 28 92 3 The 3D visualization 3 1 2 Pre stored structures There are different ways to add molecules and fragments which build up a structure Double click or drag and drop molecules from the Molecules section on the right to the window mezsure eae bonds TO rae ee ra TmoleXProject job_notRun_2 Y 4 alcohols 1 butanol sdf 2 propenol sdf 1 ethanol sdf geraniol sdf fa aie dol sdf 3 a sE a dl amino acids gt de rarhanwle F 4 E 00000 cose l The molecules in the right part of the window are by default taken from the fragments directory of the TmoleX installation This can be changed to a user defined directory in the Tools Visual settings menu Fle View Edit Tools Display Type Wi Fragments Settings w Scan depth a Database smOlogicAppData TmoleX14 fragments Browse The files are stored in standard sdf format and a second file with the same name but sdf fr ending is being generated The fr file con
25. 13 z convinfo energy change actual value 0 000 threshold 0 1000E 05 geom gradient actual value 0 3718E 04 threshold 0 1000E 02 1158 1621452220 dE dxyz 0 076610 1158 1693245640 dE dxyz 0 043440 1158 1697110240 dE dxyz 0 029705 1158 1730026110 dE dxyz 0 018724 1158 1738758140 dE dxyz 0 014882 1158 1744200210 dE dxyz 0 006320 1158 1746926290 dE dxyz 0 006530 1158 1749271050 dE dxyz 0 007789 What next 1158 1751288820 dE dxyz 0 007557 1158 1754120080 dE dxyz 0 003472 Start new job with current data as input 1158 1756717060 dE dxyz 0 003944 1158 1760774160 Save as job template for further usage sarn sorna v 44444444 y J Page 53 92 3 The 3D visualization The total energies for the optimization steps can by viewed here File View Edit Tools DisplayType Window Help laa e s a Ko ti Q a Gradients Vib Modes J Internal Coords Y Builder Orbital Viewer Scan J TmoleXProject job_GEO_13 gradient x 4 Number of atoms 28 Number of bonds 29 b Objects Gradient v J E visible Arrow stale 50 Energy 1158 1769 OOOO een os left mouse button Click a handle and drag to rotate the selection right mouse button rotate MMB move Wheel zoom The different geometry can also be viewed as a movie by using the play buttons or moving the slider The smaller
26. 29705 SCF energy 1158 1730026110 dE dxyz 0 018724 SCF energy 1158 1738758140 dE dxyz 0 014882 tes las UV Vis Spectrum SCF energy 1158 1621452220 dE dxyz 0 076610 z tas EAT ls Raman Spectrum Spectrum SCF energy 1158 1744200210 dE dxyz 0 006320 SCF energy 1158 1746926290 dE dxyz 0 006530 SCF energy 1158 1749271050 dE dxyz 0 007789 What next SCF energy 1158 1751288820 dE dxyz 0 007557 SCF energy 1158 1754120080 dE dxyz 0 003472 Start new job with current data as input SCF energy 1158 1756717060 dE dxyz 0 003944 SCF energy 1158 1760774160 dE dxyz 0 005914 J Save as job template for further usage 444144 Page 55 92 3 The 3D visualization The new window which opens allows you to generate 3D data for visualization as well as to start the 3D viewer with previously or newly generated data Sel HOMO LUMO E 1 LUMO 4 LUMO 3 LUMO 2 LUMO 1 LUMO HOMO HOMO 1 HOMO 2 HOMO 3 HOMO 4 IE m pa erret __ __ __ __ __ 2 Choose Density and Electrostatic Properties Sel Plot propertyname Plot flename Ground state total density ist derivative of total density 2nd derivative of total density Laplacian of total density Kinetic energy density Electrostatic potential Electric field Gradient of electric field Electrostatic potential color coded on density isos agt eae Re ee eae hg hg L
27. 43 11 AM Jun 4 2014 10 57 53 AM __ Stop Jun 2 2014 4 07 30 PM Jun 3 2014 9 55 27 PM jun 4 2014 10 01 58 AM Jun 4 2014 10 22 04 AM Jun 4 2014 10 26 53 AM Jun 4 2014 10 40 46 AM Jun 4 2014 10 47 00 AM Running _ Type GEO DFT RI B P charge 0 c1 def SV P GE GEO DFT Disp RI charge 0 C1 def SV P SP DFT RI B P charge 0 c1 def SV P FREQ SP DFT RI B P charge 0 c1 def SV P NMR SP DFT RI B P charge 0 C1 def SV P EX GEO DFT RI B P charge 0 c1 def SV P GE GEO DFT RI B P charge 0 C1 def SV P G OPT FREQ xml l O Ei Energy vs Geometry cycle T a i SCFKIN SCFPOT Y scan_0010 Po uae Y scan_0011 Y scan_0012 v job_TEMPLATE_14 job_0000 1 2 3 4 5 194 2039480590 194 2047077801 194 2047697520 194 2047756935 194 2047781207 192 2805999062 192 1912148110 192 1688533165 192 1673543536 192 1686932171 386 4845479652 386 3959225912 386 3736230686 386 3721300471 386 3734713378 194 2040 194 2041 194 2042 job_0001 194 2043 194 2039480590 194 2047077801 194 2047697520 194 2047756935 0 028814 0 008648 0 002675 0 001452 194 2044 E a ow II a A A 1 194 2045 194 2046 194 2047 Page 73 92 6 Job Templates 6 3 Results of job templates Multi template jobs will create sub directories for each individual job Selecting an individual job will present the results of this step as for a usual non template jo
28. 5 sv Ot Save Export current coordinates in various formats Save current job to disk Open the directory of the current job in the default file browser of your OS Open molecular viewer Can also be used to build new molecules Jobs running local 0 4 remote 9 TmoleX can run jobs on your local machine as well as on remote systems It also includes a simple queuing system By clicking on either the local or the remote button a list of running jobs will open Memory used for Tmolex _103 4 124 1 MB System 0 0 6236 2 MB The memory usage of TmoleX itself and the jobs that are running on your local system is displayed here click on the TmoleX button the yellow one in this example to free unused memory starts Java garbage collector Page 12 92 2 A quick tour 2 4 The sections TmoleX is structured as an interactive TURBOMOLE input program similar to the define program which generates the input on the command line 1 JOn the left you will find a list of open projects and jobs of each project 2 Jon the top the general task menu Geometry Atomic Attributes Molecular Attributes etc 3 in the main frame the data assigned to the chosen task File Edit Templates Results Extras Tools Help H i 8 open 30 Molecular Builder Jobs running local 0 8 Memory used for TmoleX 47 5 70 2MB System 0 0 17087 9 MB Choose Job Template Y Charge Use from input w G 2
29. 7 0 and newer w TURBOMOLE directory Status of emote system Currently no running jobs from this session of Tmolex15 max avail CPUs unknown number of CPUs in use Use queuing system A simple click on Start will start the job on the chosen system The job list shows on which machine a calculation has been started or is still running The right mouse button menu in this list allows to kill a job also on a remote machine Y aniline 12 job_SCAN_11 GEO DFT RI B P charge 0 C1 def SV Jun 4 2014 10 43 Jun4 2014 10 47 Local gt lo job _BATCH_17 14 job_TEMPLAT OPT FREQ xml Jun 4 2014 10 57 Jun4 2014 10 59 Local C job_GEO_18 15 job_BATCH_15 COSMO BP SVP xml Jun 4 2014 11 10 Jun4 2014 11 18 Local 17 job_BATCH_17 OPT FREQ xml Jun 4 2014 11 39 Jun4 2014 11 49 10 0 0 250 18 job_GEO_18 GEO DFT RI B P charge 0 C1 def SV Jun 4 2014 12 15 Running 10 0 0 205 Note that the Stop time is not the end of the job itself but the time when TmoleX noticed that the job has finished Page 87 92 8 Remote jobs 8 4 Using a queuing system on a remote cluster Remote machines Y ff Default tmolex210 0 0 205 tmolex 10 0 0 207 Machine IP 10 0 0 207 User tmolex Fassword He Group name Default Identification tmolex 10 0 0 207 Check Fassword Settings l Test remote system Work directory jac fimolexTmolex_Jobs TURBOMOLE directory software T
30. 70 2 00645 43 81 2 19129 56 45 1 34525 86 82 0 69893 105 33 4 48697 128 16 11 12831 164 48 10 12821 168 29 4 25712 209 66 5 53188 230 09 0 33617 241 17 0 12354 276 95 3 12643 285 59 3 19482 301 60 6 23896 311 26 4 97524 327 85 1 50038 337 42 12 16861 a S 50 Arrows visible Amplitude 1 Frames 242 _ Calculate bonds Select one or several modes first Use the play buttons and or the slider to see the vibration Page 62 92 4 Properties 4 2 IR spectrum Use the ES IR Spectrum to open the IR spectrum 60 0 294 7179 3825 7143 0 0 4790 O Lorentzian ant D A aa illu il 500 1 000 1 500 2 000 2 500 3 000 1 cm Standard deviation for the broadening Gaussians or Lorentzains a frequency shift number of sampling points etc can be entered The tables with the original data line spectrum and calculated data points that define the broadened lines can be used to copy and paste the data to a spread sheet or a statistics program Page 63 92 4 Properties 4 3 Nuclear magnetic shielding For the calculation of nuclear shieldings choose this job type and simply run it Start Calculation Job type Geometry Optimization Spectra amp Excited States Single Point P Single Point Properties gt Potential Energy Scan PES P Transition State Search Templates Batch processing IR vibratio
31. Build complex molecules by Merging fTagIMentS ccccooccccccccnccncccnnncnncnnnnconncnnnononononnnonnrnnonannnonanenannnos 34 3 01 DUIGING SICD DY PA o CE A se duaceuica daly ed bmaneninns Genet uncuneasnaubniawiae 39 9012 Change Dond ends oca 41 310 0 Change to ON oa 42 3 Change Dond andina a lidad 43 Sl BUldiNA Step DY SIE Dil td A A A a 44 310 FE OPUNMIZAUION st iooilcies is 46 3 9 Labels and M aSuremMmentts cccccscccssscceeeecseeecseesesecseneeeeeesseeeeueeseueeseusessesesseeeeseeseueessaeesetensenees 47 310 MOVING Rotating o Caldo idas 50 911 Ne gradlentMeWe Ri dia 53 JIZ a A O A ulate e de 55 o A a ete loll coe 61 Al VIDratonal Tequendama li o a a aaa 61 ASS PEC a ld cnneust en srae dic 63 4 90 Nuclear magqnetic SnISIdIMO ica da a E E E 64 4 4 UVNis and CD spectra D DD EW since cc ccavcctnaie sentec aececoeats canadears tncp saceccbsasesenindss asmee esate Tera ra 65 5 Constrained optimization ANd Scan JODS ccccceececseececceeeeceusecceceecueccseueescueecsaueecsuseessaeeeseseessaeeseeenaes 66 5 1 Defining fixed internal COOFrdiNates cccconccoconncocononoconnnononncconcnononononannnononnnonnrnnonannnnnnnnnnnnnennnnanennns 66 diz Se Inte mal coordinato Sa A 67 5 9 tant constrained OpimizalO hed ote ie ee eee ei oes 68 5 4 scan along an Internal cordiale ui ncedneteteaat acl aie en eds 69 5 5 Scan along several internal COOrdiNates cccoccccoconnccocnnoconnccco
32. Import Coordinate File Open 3D Molecular Builder f vw Symmetry Internal coordinates Current point group ci Constraints Value Max tolerance 0 001 u Autodetect Symmetry New point group cl Apply New Point Group 1 2 3 4 5 6 7 8 9 5 p pa oie ioc ei ieicgci ei ieig c ca sc LIT IZT Ss Si SIAILAIAIATATA Page 13 92 2 A quick tour The input is divided into four different sections Geometry The kind of job or property that shall be calculated can be set in the Start Job panel Startjob gt Results after a successful run can be viewed and further investigated in the Results panel Results You should follow the menu structure in the main frame from left to right The traffic light colors are indicating which steps have been accomplished and for which steps input is needed Color code Red No valid data is available User action required Yellow Default settings available unchecked by user so far Green The data is correct or user did already visit this section Grey Section is currently not available like Results for a job which did not run yet Page 14 92 2 A quick tour 2 5 An illustrative example Part 2 2 5 1 Geometry panel After reading in the coordinates you are in the S omety f section Here you can choose the symmetry create internal coordinates add atoms or modify the structure Fil
33. Multiple Jobs Comparison Movie Y job_SP_7 Y job_SP_8 Unit Hartree Open Scan Movie Ha It O Y job_SCAN_9 E Y scan_0000 y a alue 154 9057 N Y scan_0001 Scan directory Zero tors H9 08 C3 Energy puppan S ES scan_0000 DEO 154 9057 0 154 9059 x Scan scan_0001 9 154 9059E0 154 9060 Y scan_0004 Y scan 0005 scan_0002 20 154 9064E0 154 9061 Y scan 0006 scan_0003 30 154 9071E0 154 9062 3J job_SCAN_11 scan_0004 40 154 9078E0 154 9063 Y scan_0000 scan_0005 50 154 9083E0 154 9064 Y scan_0001 scan_0006 60 154 9085E0 154 9065 Y scan_0002 scan_0007 70 154 9083E0 154 9066 Y scan_0003 scan_0008 80 154 9079E0 154 9067 Y scan_0004 scan_0009 90 154 9072E0 154 9068 f E scan_0010 100 154 9066 0 154 9069 Y scan 0007 scan_0011 110 154 9061E0 154 9070 ie scan_0012 120 154 9058E0 154 9071 Y scan_0008 154 9072 Y scan_0009 ds Y scan_0010 154 9073 Y scan_0012 154 9075 154 9076 154 9077 154 9078 154 9079 154 9080 154 9081 154 9082 154 9083 154 9084 10 lt lt Previous Manage Job s Ll yx Apply Job Template Start Job Results The final optimized structures are stored for each of the scan points in a multi coord file similar to the gradient view This can be viewed like a movie with the button Open Scan Movie 5 5 Scan along several internal coordinates The number of internal coordinates which can be used for scans is only limited by technical issues If
34. O_1 job_GEO_5 _Jjob_SP_6 job_SP_7 __ job_SP_8 Y job_SCAN_9 v 7 job_SCAN_11 J scan_0000 J scan_0001 _ scan_0002 J scan_0003 scan_0004 _J scan_0005 scan_0006 _ scan_0007 J scan_0008 Project Name Job Name 2D structure Number of atoms Basis functions Charge Multiplicity Freeze Level of theory Cosmo Energy Dipole moment eran nnna Y Zero point vib ener gt job_0000 job_0001 TmoleXProject TmoleXProject job_0000 job_0001 N 10 14 def SV P def SV P 0 0 0 0 Singlet Singlet off off DFT Disp DFT D3 DFT Disp DFT D3 off off 135 062169 287 413943 1 351271 0 113743 job_0001 TmolexProject job_0001 A 12 def SV P 0 0 Singlet off DFT Disp DFT D3 off 194 204778 0 104456 232 075794 Additional results can be added to the table by selecting the jobs on the left side in the project list Page 92 92
35. URBOMOLE_70 TURBOMOLE Number of CPUs forjob s 1 Checkremotesystemevery 1 min TURBOMOLE version unkown Status of remote system Currently no running jobs from this session of TmoleX15 max avail CPUs eno number of CPUs in use p Script before job execution without bin sh gsub Check status gstat automatically E add PARA_ARCH MPI Script after job execution E add PARNODES number of CPUs Currently PBS LSF and SGE are successfully tested Activate the queue option in the remote job start panel To be able to support as many queuing systems as possible the number of options is kept very small 1 Submit with this is the command that is used on the given remote system to submit a job to the queue Here you can give just the name but also options For PBS and SGE like queuing systems qsub is the default For LSF it should be bsub lt Page 88 92 8 Remote jobs For unsupported queuing systems it is possible to write a script on the remote cluster that sets the number of CPUs and the list of nodes that shall be used for the job and submits the start script to the queue The name and probably the path to this self written script can then be entered in this field 2 Check status this is the command that is called on the remote system if the View run status option from the right mouse menu of the Job administration is chosen The output of the status command is shown directly underneath the
36. amp Prepare to Run Manage Job s A a ae Yee eae Ex File Edit Templates Results Extras Tools Help 7 ii a a m Ga 9 open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmole v E ProjectList System 0 0 6296 2 MB Atomic Attributes gt Molecular Attributes gt Mod Stattlob gt Results Y 5 TmoleXProject 7 fee Y job_GEO_1 Choose Job Template v Charge Applygpob Template b gt Y job_GEO_5 a A Y job_SP_6 Coords amp Sym Multiple Coordinates Y job_SP_7 Y job_SP_8 add Molecule 5 Delete Molegfle pis a a Number Name Charg Image cick to view modfy gt job_TEMPLATE_14 methylamine 1 methylamine 0 ethylamine propylamine aniline VON 2 ethylamine 0 3 propylamine 0 4 aniline 0 l Apply Job Template amp Prepare to Run Manage Job s The charge may or may not be imported correctly so check and eventually change the charges in the table The multiplicity can also be changed but it is recommended not to do that since TmoleX will use the TURBOMOLE default it determines from a H ckel calculation lons are shown in different background colours a quick look on the table should to sufficient to identify non neutral compounds Double click on a graphical representation of the molecules to open the builder Page 76 92 7 Batch processing
37. ased See the TURBOMOLE manual for details about DIIS Page 21 92 2 A quick tour 2 5 5 Start Job Select kind of job and start it In the SitartJob panel a single point energy calculation can be started File Edit Templates Results Extras Tools Help 0 D Ge Se EH 6 9 open 30 Molecular Builder v fd Projectiist Y E TmolexProject ALOT ALCriDUCes a Fe job_notRun_1 Choose Job Template Y Charge Use from input w Apply Job Template Start Calculation Method l Job type Level DFT Functional b p Y RI Geometry Optimization gt Basis set def SV P Symmetry C1 Convergence Parameter Potential Energy Scan PES gt Energy 10 Density Transition State Search gt Templates gt Use resources Batch processing gt Memory used for 500 0 Disk 0 No of CPUs 1 E Delete scratch files after run Save and Run Run local will start the calculation in the present directory Save writes the complete input to disk for further use on the command line or later usage if needed Saving the job to a directory will also add a script call start job to the selected directory which can be used to start the job on the command line Run network starts the calculation on a remote Linux Unix computer see chapter 8 Page 22 92 2 A quick tour Click through the Job type options to see what kind of jobs are supported by TmoleX File Edit Templates Resul
38. b Selecting the template itself in the job tree will give a summary as table TmoleX 4 0 TmoleXProject L fel 13 File Edit Templates Results Extras Tools Help LP pp 2 g Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex J OPT FREQ xml Charge Apply Job Template Job Results Scan job result Job Comparison Results Multiple Jobs Comparison Movie job_0000 job_0001 System 0 0 6296 2 MB v E ProjectList v 5 TmoleXProject Y job_GEO_1 Y job_GEO_5 Y job_SP_6 Y job_SP_7 Y job_SP_8 Y job_SCAN_9 Y scan_0000 Project Name TmolexProject TmolexProject Y scan_0001 Job Name job_0000 job_0001 Jf scan_0002 Y scan_0003 Y scan_0005 Y scan_0006 Number of atoms O 12 a 12 O E Ppp Basis functions def SV P def SV P Y scan 0001 Charge 0 0 0 0 Y scan_0002 Multiplicity Singlet Singlet Y scan_0003 Freeze off off x scan_0004 Level of theory DFT Disp DFT D3 BJ damping Grimme et al 201 DFT Disp DFT D3 BJ damping Grimme et al 201 Y scan_0005 Cosmo off off Y scan_0006 Energy 194 204778 194 204778 Y scan_0007 Dipole moment 1 526881 A or poon Zero point vib energy 0 104456 Y scan_0010 Y scan_0011 Y scan_0012 fe job_TEMPLATE_14 Y job_0000 Y job_0001 Manage Job s Here an example of ethanol the job template was GEO OPT from the predefined list of job templates Page 74 92
39. bmit scripts or ask you system administrator Page 90 92 8 Remote jobs 5 Script after job execution The script that is being submitted to the queue can be extended with the entries in this field Useful if you want to do some post processing on the remote machine Say you are running a geometry optimization and submit the following script to the queue lt Page 91 92 9 Combining results 9 Combining results To combine and collect results from different jobs select different jobs from the job tree by holding lt Shift gt or lt Control gt key and clicking on the jobs then use the right mouse button and select export results v gt v W v v E ProjectList v 5 TmoleXProject Y job_GEO_1 i Y job_GEO_5 Y Job Results Sc Y job_SP_7 Y job_SP_8 Type of Calculatior v job_SCAN_9 Y scan_0000 Y ES Jf scan_0002 Y scan_0003 Energy Y scan_0004 zero point VIBRAT Y scan_0005 SCF energy cn 0006 SCF E vib0 v job_SCAN_11 1 job_TEMPLATE_14 Y job_0000 a Py job_BATCH_15 Y methylamine ethylamine Vibrational Modes Y propylamine 2 a Y aniline 23 Y job_BATCH_17 24 gt TmolexProject_r 25 jara 26 gt gt TmolexPrc HRS gt V TmoleXPrc Generate new Batch Job Y job_GEO_18 job_GEO_19 VU yy ow TmoleX will generate a table with the most important data Save as Excel v E ProjectList v 5 TmolexProject _ job_GE
40. button and moving the mouse to the right or up will move along the positive direction plus x y z values and moving the mouse down or to the left will decrease the coordinates no matter from which direction you are looking at the structure This can sometimes lead to the fact that moving for example the mouse to the left will move the fragment to the right because you are looking at the structure from behind o Again in addition to the absolute directions x y z you can move the selected atoms along the direction that corresponds to the 2D coordinates of your screen Right Left and Up Down Click on along view to reset the Right and Up direction to your current view on the structure e Finally the scale tool e key r scales or resizes relative distances between atoms Add a benzene ring select it and use this tool to see what it does Page 52 92 3 The 3D visualization 3 11 The gradient viewer Once you have completed a geometry optimization you can open the gradient viewer from the results panel File Edit Templates Results Extras Tools Help 3 D 555 H GB open 30 Molecular Builder ISSN System 0 0 17087 9 M6 v la P 2 tl e t 4 Y E TmoleXProject A A eee Y job_GEO_1 Choose Job Template Y Charge Use from input w Apply Job Template Y job_sP_2 Y job_sP_3 Job Results Type of Calculation Geometry Optimization pops Geometry Convergence Criteria job_GEO_
41. dant coordinate usage must be activated when starting a geometry optimization Be careful with linear combinations several lines of definitions for one internal coordinate while they can be fixed this is usually not what one really wants There is a possibility to visualize the set of internal redundant from within the Geometry panel 5 3 Start constrained optimization A constrained search is automatically done if a usual geometry optimization job is started while having internal or Cartesian coordinates fixed TmoleX will show a message in the panel whenever such jobs are started 4 TmoleX 4 0 TmoleXProject halla iea File Edit Templates Results Extras Tools Help io a pa PD Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for TmoleX 117 2 294 6 MB System 0 0 6296 2 MB uy je is Pe y E ProjectList Geometry Molecular Attributes Start Job Y 5 TmoleXProject i paenewscncnnnrccnenscncnnnratnswsnsnsnsasnensnnwensnsrnnnenenannees en enss tnracwsnsnsnsnsnraenenens Y job_GEO_1 Choose Job Template w Charge w Apply Job Template Y job_GEO_5 Y job_SP_6 Start Calculation Y job_SP_7 Y job_SP_8 Job type alas Job_notRun_2 Geometry Optimization Ground state Level i Functional b p Spectra amp Excited States gt Single Point gt i y Basis set def SV P Symmetry C1 Single Point Properties gt Potential Energy Scan PES gt Convergene e E ergy 1
42. der Jobs running local 1 4 remote O Memory used for Tmokx __98 5 152 0 MB System 500 0 6296 2 MB M Fre job_GEO_1 Choose Job Template w Apply Job Template Type Start Stop job_GEO_1 GEO DA May 30 2014 4 10 5 Running job GEO choose Project Job Type gives Start Stop for indicates a in ProjectList to a very short timings and the geometry get a list of all description of status if job is optimization jobs the most still running important settings While the job is running and if you select the project itself in the project list on the left the lower part of the TmoleX window will show the current status of the selected job there is just one job on the example above Click on the name of the Project in the ProjectList and use the right mouse menu in the Jobs section to close remove just from the list let all files on disk stop stop running jobs let files on disk delete delete job from the list and delete the files from disk jobs View Job directory will open the default file browser on your system with the directory where the selected job is running or was running View run status can be chosen for running jobs y fl Projectiist File Edit Templates Results Extras Tools Help i Mis pe nE H be gp Open 3D Molecular Builder Y 5 TmolexProject f mea Choose Je Stop this Job View Job Directory Name Open Shell Ml 1 job_GEO_1 Delete this Job View Run Status Th
43. deviation during check Bohr def Sv P gt Multiplicity Automatic RHF UHF for post HF in Hartree DFT D3 BJ damping Grimme et al 2011 SCF convergence Max number of SCF iterations 250 SCF energy 10 6 SCF density Max no of cycles 4 Use internal redundant coordinates COSMO settings COSMO On Geometry Optimization Ground state 250 Save as Template The settings are quite self explaining Read in existing template to modify or apply Create new job template Click on a to add a job to the workflow MOPAC pre optimization only possible in first job Make sure not to switch on the symmetry check in the following Turbomole jobs The settings here are the same as in the different TmoleX panels Save the template or apply it without saving But at this point TmoleX does not check for consistency of different settings So please do first a usual job run it and check if the combinations are possible Defining multiple jobs in one job template will tell TmoleX to run them one after the other using the coordinates of the preceding step job 1 Use final coordinates of job 1 Use final coordinates p job2 of job 2 Page 71 92 p gt job 3 Use final coordinates of job 3 6 Job Templates A typical work flow would be RI DFT geometry o
44. e In this example the charge field is empty so TmoleX will use the charges printed in the table Otherwise they are overwritten Before starting a batch job you have to click on 4Pply Job Template to assign all settings of the template to your individual jobs Possible errors or problems can thus be detected before the whole batch is started or sent to a remote system This process can take some time depending on the number and size of the molecules as well as the number of steps defined in your template Geometry tomic A r Attribui 3 Start Job GEO OPT quick xml Charge 3 Progress orbital generation 50 Stop Calculation After applying the job template a short overview is printed in the Start Job section Batch processing Batch Job Template Use resources n ENG Lt Memory used for 500 0 MB C YUsersiTmoleX 1COSMONOGICA Job Name Job1 Job2 Disk 0 MB for HF Symmetry check on on No of CPUs 1 Basis functions def Sv P def SV P l Charge used from input used from input 1 Delete scratch files after run Multiplicity Automatic RHF UHF Automatic RHF UHF Freeze off off Level of theory DFT Disp DFT D3 BJ damping DFT Disp DFT D3 BJ damping Cosmo off off Job Type GEO FREQ Save and Run Run local Save Run network Page 78 92 7 Batch processing 7 3 Run local or remote batch jobs After a job template has been applied and TmoleX has finished to generate the input fi
45. e Edit Templates Results Extras Tools Help 0 157656 H 65 9 open 30 Molecular Bulder Jobsrumming local 0 8 remote a e ba Projectlist Metnoc Start Job v 3 TmolexProject tarerarerarerareearerarerarerarerarerarrrarerarerarererreareraereareeeneearerertarerarzrarzearaeanra Choose Job Template Y Charge Use from input w Apply Job Template PASA Coords amp Sym 25 Import Coordinate File Open 30 Molecular Builder A ran D PJ smes to 3D Units Aw Atomic Symmetry Internal coordinates Number ofatoms 12 Constrai Current point group ci Value Max tolerance 0 001 au AutodetectSymmetry New Atom l New point group ci Apply New Point Group oon Dm bh QU HN Src zz SI LIAIATA A AITA oo o ooococo9dce9dbOoO amp Page 15 92 2 A quick tour 2 5 2 Basis set panel File Edit Templates Results Extras Tools Help 0 D Ge Ge H 6 9 open 30 Molecular Builder Jobs running local 0 8 1 v Projecttist Atomic Attributes __ Y Ss TmoleXProject I aaee F Choose Job Template y Charge Use from input v Apply Job Template A Basis Sets Basis Functions 102 Basis Set for all Atoms Basis set def Sv P def Sv P def Sv P def Sv P def SV P def Sv P def Sv P def Sv P def Sv P def Sv P def Sv P def Sv P def Sv P l Basis for elements Show ECP C def sv P H def sv P E we ON DH PWN He
46. e ee Re eee ae he hg View all in one Calculate selected View selected The upper section is the list of molecular orbitals the lower section is for electrostatic and density derived properties For each of the properties there are two options quick and a high res The first one is to generate the data on a coarse grid to keep the time for generating the 3D files low This is useful to quickly check the shape and position of orbitals densities etc The second option generates the data on a finer grid generating smoother surfaces but can require significantly more CPU time to generate the data This is recommended for graphics aimed for publication Page 56 92 3 The 3D visualization There are three possibilities to generate 3D data 1 directly click on one of the buttons and TmoleX will directly start to generate the data 2 set checks in the first column for each orbital and property you want to visualize and then click on Calculate selected Choose Molecular Orbital s Sel Peeeeeee88 8 NNNNNOG OSSOO sf Choose Density and Electrostatic Properties Sel Plot propertyname Ground state total density 1st derivative of total density 2nd derivative of total density Laplacian of total density Kinetic energy density Electrostatic potential Electric field Gradient of electric field Electrostatic potential color coded on density isos des Es ee uE uds ads ad at a
47. e progress and status of all calculation belonging to your project which are currently running or ran Page 25 92 2 A quick tour before can be accessed via the Job Administration by clicking on the project name itself instead of a job within the project After starting a first job you can instantly set up and even launch a new one For performance considerations you will however prefer running only one job at a time in most cases Note TmoleX does not yet cover all possible kinds of calculations and input options that TURBOMOLE offers If you need additional options but want to use TmoleX you can manually edit the control file Please refer to the TURBOMOLE manual for further information Internal simple queuing system Set the number of cores of your machine in the Extras Settings menu Then TmoleX will take care of the number of jobs you are starting Memory used for Tmolex 96 6 171 7 MB System 500 0 6296 2 MB Jobs running local 1 4 remote O The green section is related to the memory usage First by TmoleX itself click on the button to start Java s garbage collector to give free unused memory and then by the jobs which are running estimated from your memory settings when starting those jobs The grey section shows the number of local and remote jobs Note that only jobs from open projects are shown closing a project with running jobs will is not recommended as TmoleX w
48. ergence criteria Energy 6 101 Hartree Save and Run Gradient norm 3 dE dxyz 107 Hartree Bohr AR Max no of cycles 50 a Use internal redundant coordinates Run network lt lt Previous Manage Job s The list of fixed internal coordinates is shown in the PES scan Options section To define a new fixed internal coordinates use the Create New Constraints by Selecting Bond s button This is not needed if you did that in the builder already The different options how the start geometries are generated are described in the panel itself Unrelaxed scans and relaxed scans are possible single point or geometry optimization calculations will be done We recommend to use the Use current structure for all option because if one of the steps fail the remaining jobs will have problems too otherwise Page 69 92 5 2 Use internal coordinates The job can then be started as usual also as a remote calculation A typical result is shown here aren x Memory used for Tmolex 121 2 175 0 MB System 0 0 6296 2 MB 4 TmoleX 4 0 TmoleXProject File Edit Templates Results Extras Tools Help pl pe E a aa H g Open 3D Molecular Builder Jobs running local 0 4 remote 0 y E ProjectList Atomic Attributes Molecular Attributes Y 5 TmoleXProject Y job_GEO_1 Choose Job Template y Charge Y job_GEO_5 Y job_SP_6 Job Results Scan job result Job Comparison Results
49. fined as fixed 4 TmoleX 4 0 TmoleXProject E File Edit Templates Results Extras Tools Help 2s A H az g Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 118 1 270 5 MB System 0 0 6296 2 MB y E ProjectList Molecular Attributes Start Job Y 5 TmolexProject Y job_GEO_1 Choose Job Template Apply Job Template Y job_GEO_5 Y job_SP_6 Start Calculation job_SP_7 Se Method joD_SP_ Single Point gt job_notRun_9 i Level DFT Single Point Properties gt Aen bp Potential Energy Scan PES Potential energy scan a Basis set def SV P Symmetry C1 Templates gt Convergence Parameter Batch processing gt Energy ae Density Potential Energy Scan PES Options List of all fixed constraints Constraints Value Start End Stepsize Constraint stre C1 0 1 525 3 525 0 5 Use resources Memory used for c MB Create New Constraints by Selecting Bond s Disk MB for HF Unrelaxed scan no geometry optimization Relaxed scan geometry optimization at each point No of CPUs 1 Use current structure far all Generate each start structure from previous step Delete scratch files after run This will cause TmoleX to generate start structures for all This will cause TmoleX to generate just the first structure steps of the scan directly from the current structure then take the optimized coordinates for the next steps later on Options Conv
50. for example the number of constraints is relative to the number of degrees of freedom very high TmoleX might not be able to generate all intermediate structures of all combinations due to steric reasons It is also possible to combine constraints like fixing an angle to a certain value with scans If the number of internal scan coordinates is larger than one TmoleX will not show a graph of the result but just the table with the values of each internal coordinate and the total energy in the last column This table can be exported to a spread sheet program or other data analysis tools Page 70 92 6 Job Templates 6 Job Templates 6 1 Define job templates TmoleX gives you the possibility to save the most important settings of your jobs like basis set method or job type to a template This helps to reduce the time needed for an input preparation if the same kind of job has to be performed for a set of molecules To read modify or create a job template choose Templates from the TmoleX menu Choose Template Load template OPT FREQ i I New Template Jobi X Settings Turbomole Turbomole Geometry Symmetry Basis set Molecular charge Method Level Functional Dispersion conv criteria Job type Job Type Your choice Jb2 X L Atomic Attributes Molecular Orbitals Use from input Freezing point Hartree 9 99999999E8 DFT Disp BP86 max allowed
51. gle jobs which are finished but not yet transferred back to your local desktop machine the icon switches to E poo nn i le e job_BATCH_17 4 TmolexProject_meti 2 jobo 2 jobo 4 TmolexProject_ethy 2 job 0 ge jobo Y 7 TmolexProject_propy job_0000 B job_0001 Y TmolexProject_aniline job_0000 job_0001 Page 79 92 7 Batch processing Using many cores or CPUs on your local system As you can see in the screen shot printed above several different jobs can run at the same time when a batch job is being used To be able to use several CPUs on your system you have to tell TmoleX how many of them you allow the program to use on your local machine To do that just select the Extra Settings entry in the menu and you will get a new window 4 TmoleX settings Display settings Font type Font size 11 v File settings User directory C Users Tmolex Browse System Available processors Total physical memory size 6296 2 MB Check memory Activate netbook option scrollbars Visibility of hydrogens in export table O Default with hydrogens without hydrogens TURBOMOLE Defaults Optimization Settings Energy convergence 6 Gradient norm 3 Max no of cycles 50 Cancel Save Set the number of available processes here but it is recommended not to use all available cores to let at least one of
52. he 3D visualization 3 5 Easy building Paint tool A quite handy way to build is the paint tool Fle View Edit o a which can be chosen by clicking on the Y button or hitting the D key on the keyboard In the paint modus select an atom or a molecule from the Molecules Atoms section in the builder Molecules Atoms sp dif lajn li Be E 00 K Ca Re Sr mij ir ple a a x 5 2 5 7 Cs Ba Fr Ra Hybridisation _sp3 tetrahedral 3 X H This will change your cursor to the element symbol to add a nitro group resp Click on the background to add the atom or molecule or click on an existing atom to replace it with the selected atom fragment Click on the hydrogen Page 33 92 3 The 3D visualization 3 6 Build complex molecules by merging fragments a Load two molecules select one atom from each of two different fragments BondiAtom Style Labels e Edit additional label a Invert selection Measure distance Translate Rotate Scale Create bond Merge overlapping atoms Add atom at center Create group b Use the right mouse button and select the Merge option TmoleX will join the two fragments and re arrange the resulting structure such that the overlap of the atoms is minimal Page 34 92 3 The 3D visualization To merge two fragments which are not just connected by one bond a more powerf
53. ill loose the connection and might not be able to correctly reopen them Whenever the number of running local jobs is exceeded TmoleX will start the next job only after another one has finished Several jobs can be started that way without blocking your system The jobs that are scheduled for running are shown with an own icon in the job list Page 26 92 3 The 3D visualization 3 The 3D visualization 3 1 The 3D builder To open the molecular builder click on either the button in the tool bar or the button in the Geometry panel of Tmolex Fie Edit Templates Results Extras Tog Help DOES as eo Ra l i Projectiist Y 3 TmolexProject i Y job SEO_1 ES job_notRun_2 Molecular Attributes mm Charge Use from input Y Current point group cl Max tolerance 0 001 Autodetect Symmetry New Atom New point group cl Apply New Point Group Delete Selected Atoms The molecule builder can be used most conveniently by starting from fragments and modifying these Double click on a fragment to import it in the builder B Fie View Edit Tool Display Type Window Help qe a DO 212929 a Q2 oleXProject job_notRun_2 Number of bonds 12 imidazole sdf indole sdf pyrazole sdf lei alll 00000 left mouse button Click or drag to select right mouse button rotate MMB move wheel zoom Page 27 92 3 The 3D visualization 3
54. ing processes is shown If you did set the number of total CPUs on the remote system as described on the last page it is also shown here as available CPUs The three entires are e current number of CPUs in use right now e 5min ago number of CPUs in use approximately 5 minutes ago e 15min ago number of CPUs in use approximately 15 minutes ago This gives quite a helpful hint how occupied the system already is and whether or not some new jobs have been started recently or how many old jobs stopped in the last 15 minutes If you activate the Show expert information check box you will see the detailed output of top which users run which jobs on the machine how much CPU time and how much memory they use In the example given here only the user tmolex is running jobs entries with significant CPU values Page 82 92 7 Batch processing 7 4 Visualize and export results of batch jobs The results of finished batch jobs are given as tables in the Results section Each sub job has an own tab in the table y E ProjectList a omic Attribut al yy E may E Y 5 TmolexProject PS TL EE A TT Y job_GEO_1 Choose Job Template w Charge w Apply Job Template Y job_GEO_5 Y job_SP_6 Y job_SP_7 Y job_SP_8 7 job_SCAN_9 y job_SCAN_11 v job_TEMPLATE_14 Level of theory rimmeetal 2011 b p Functional b p My job_BATCH_15 Y methylamine Export Files Save as Excel Y ethylamine LL SS SS SSL Y
55. itute with Charge 0 CH2 4 OH Change element Coordinate As connecting atom Arrange Saturate Yoridisatio custom Saturate Arrange d 2 propenol ethoxy gerany l ji d d Paste Copy Cut Delete alacati custom atom Open t edit ICON Ol J 1 butanol sdf 2 nronenolLsdf Choosing Attach with custom atom will open the structure of the fragment in an own window Left click the connecting atom Just click with the left mouse button on the atom one of the hydrogens in this case to select the connecting atom Page 45 92 3 The 3D visualization 3 8 Pre optimization There are three options to pre optimize a guess structure e Unselect all objects by clicking on the background Use the right mouse button and select Saturate all Re compute bonds Set name Set fragment name Unset connect atom A simple rearrangement which minimizes the overlap of the van der Waals radii of all atoms e UFF a universal force field as implemented in TuRBomoLe can be used by clicking on the FF button a e The recommended way is to use MOPAC which is included in the default installation of TmoleX MOFA The MOPAC7 button will open a new window with several options PM3 Jl MNDO Jl MINDO 3 Transition State Search AE O Read Restrictions Show run status Start Calculation Jl Stop Calculation Ready to start Mopac optimization
56. job list 3 Script before job execution without bin sh This is the field where a usual script that is used to submit jobs to a queue can be entered Example for PBS Example for SGE Univa Grid Engine FPBS S bin bash FS S bin bash Name of your run 5 N TmoleX job PBS N TmoleX job Export environment Number of nodes to run on FS V PBS 1 nodes 1 make sure to be in the right directory Export environment Fo cwd PBS V cd PBS O WORKDIR This is a PBS SGE example for a serial run There are several things one has to take care of TmoleX will use the given entry and include it in its own settings 1 do notgivea bin line here TmoleX adds its own commands in sh format so TmoleX will add a first line containing bin sh to the final script 2 Make sure to change the directory to where the input files are copied PBS cd PBS O WORKDIR SGE FS cwd LSF cd LS SUBCWD must be somewhere in your own script 3 Ask your queuing system for the right number of CPUs this has to match the Number of CPUs field of the TmoleX setting Depending on the queuing system it will not allow a different number than what the script will start PARNODES is set by TmoleX so if you set it in this field it will be overwritten Page 89 92 8 Remote jobs 4 TURBODIR is being set by TmoleX so you do not have to enter it again here 5 The commands to start the TURBOMOLE job
57. k Most Linux Unix systems restrict the permissions for memory or disk space for each individual user for security reasons TmoleX is able to submit a script which checks for the most important settings to a remote system If machine name or IP address user name password and TURBOMOLE installation directory are set the button Check remote system can start this process TmoleX will show the results in an own output window Search for ERROR messages in case a remote system is not able to run serial or parallel TuRBOMOLE jobs The TURBOMOLE manual contains a section which helps to install the command line version on Linux Unix machines If you are not able to figure out what to change in order to use a remote system please contact the Turbomole Support Team turbomole Wcosmologic de Page 86 92 8 Remote jobs 8 3 Start a remote job Starting jobs can be done by choosing a machine in the list of saved systems El Add new Machine 4 Save Machine 4 Save Machine as Import Machine Elf Export Machine Note runs only on Linux Unix systems v J Remote machines Y Default Machine IP 10 0 0 205 P tmolex 10 0 0 205 q cn xxxexx Import Machine Clear Add New Copy Machine Default tmolex 10 0 0 205 Check Password Settings Test remote system Work directory home tmolex TmoleX_Jobs software TURBOMOLE_70 TURBOMOLE Number of CPUs for job s 1 Checkremote system every 1 min TURBOMOLE version V
58. les of all steps and for all molecules in the list the complete set of calculations can be simply started as you would start a usual job So either use the Run local button to use the system TmoleX is running on or the Run network button to submit everything to a remote system While the job is running the icons in the job list on the left side of your TmoleX window will show their current status Fi s j ob_BATCH_17 7 job_SP_7 SP DFT RI B P charge 0 c1 def SV P N Jun 4 2014 10 21 5 Jun 4 2014 10 22 04 Local gt Pa TmolexProject_methy 8 job_SP_8 SP DFT RI B P charge 0 c1 def SV P E Jun 4 2014 10 26 4 Jun 4 2014 10 26 53 Local gt TmolexProject_ethyl 10 job_SCAN_9 GEO DFT RI B P charge 0 c1 def SV P Jun 4 2014 10 38 3 Jun 4 2014 10 40 46 Local gt gt TmoleXProject_propy 12 job_SCAN_11 GEO DFT RI B P charge 0 C1 def SV P Jun 4 2014 10 43 1 Jun 4 2014 10 47 00 Local gt j TmoleXProject_aniline 14 job_TEMPLATE_14 OPT FREQ xml Jun 4 2014 10 57 5 Jun 4 2014 10 59 38 Local 15 job_BATCH_15 COSMO BP SVP xml Jun 4 2014 11 10 2 Jun 4 2014 11 18 00 Local 17 job_BATCH_17 OPT FREQ xml Jun 4 2014 11 39 1 Running 10 0 0 250 On remote systems the resulting files will only be copied back after all steps have finished to avoid too much traffic on the network TmoleX however checks from time to time which job is currently running and whether or not the whole batch is complete For sin
59. line Updates TmoleX 4 1 includes an online update system and is able to automatically perform updates This can be initiated manually by checking for updates in the help menu But TmoleX is also able to check for updates itself How often or if at all it should connect to COSMOlogic s update server can be chosen during the installation of TmoleX Setup TmoleX 4 0 0 TmoleX updates Check install4j Page 8 92 2 A quick tour 2 A quick tour 2 1 Starting the program Starting TmoleX for the first time you will get into the Welcome panel Welcome to TmoleX Version 4 1 0 We recommend to watch the video introduction first Click on New Project and select a directory on your local system to start with TmoleX Default will be a new directory called TmoleX_Project in your home folder Please choose one of the following options New Project au Open Project Online Videos How To TmoleX Documentation To start with TmoleX create a new project by klicking on New Project Alternatively open an existing project from former TmoleX versions or watch the introductive online videos first Page 9 92 2 A quick tour All projects will require a new directory on your hard disk where this directory shall be located and which name it shall have is asked in the window that pops up Look In Tmolex jchempaint Es Contacts Ly Music L COSMOlogic Picture
60. n AAA Length A 1 5343466 To scan along the coordinate activate the _ Mark for scan check box and set minimum maximum Start 1 534 Current ali the step width not the number of steps End 1 534 Current Step size 0 e Select two adjacent bonds click on the right mouse button and use the Scan freeze bond angle Page 66 92 5 1 Defining fixed internal coordinates O TmoleXProject job 5 2 T Bond Atom Style Labels Edit additional label Invert selection Measure bond angle Translate Rotate Scale Change bond angle Swap bonds Copy Cut Delete option Again on the right side you will get the same options for scan jobs as shown above e Select one or three bonds to freeze a torsion If you just select one TmoleX will take just one of the possible torsional angles If you use the Change torsion or the corresponding button on the left side of the window the value of the internal coordinate is shown and can be changed as usual with dragging the mouse while keeping the left mouse button pressed TmoleXProject job 5 2 EJ Bond Atom Style b Labels p Edit additional label Translate Rotate Scale 5 a Change torsion Copy t Delete Page 67 92 5 2 Use internal coordinates 5 2 Use internal coordinates TmoleX will automatically generate a list of internal redundant coordinates if you accept that when being asked for If you use constraints or scan jobs internal redun
61. nal frequencies UV Vis and CD vertical excitations NMR shieldings he Raman vibra j nal frequencies Optical rotations dynamic polarizability Static polarizability In the Results panel you can see the shielding constants in a text window TmoleX 4 0 TmoleXProject E X Fie Edit Templates Results Extras Tools Help N D a a EG 9 open 30 molecular Buider Jobs running local 0 4 remote 0 Memory used for Tmolex 153 2 274 1MB system 0 0 6296 2 MB y E ProjectList Geometry Atomic Attributes Method bp StartJob Results Y 5 TmoleXProject Y job_GEO_1 Choose Job Template Charge w Apply Job Template Y job_GEO_5 Y job_SP_6 Job Results Scan job result Job Comparison Results Multiple Jobs Comparison Movie WA job_SP_7 i Type of Calculation Single Point Calculation tatus mos Converged Open Viewer HOMO LUMO gap 5 139 ev Orbital Density Plot Status geometry Not performed sradient Energy o O Senergy SCF SCFKIN SCFPOT 1 232 0757937330 229 4793919515 5551856845 2 232 0765545974 229 3195622550 1 3961168523 i 3 232 0765749475 229 2916754907 461 3682504382 4 232 0765750244 229 2903224021 461 3668974264 NMR Shieldings 5 232 0765750262 229 2902310651 461 3668060912 E 6 232 0765750263 229 2902164707 461 3667914970 AS Send Open Files Output NMR Shieldings Energy nmr dft shielding constants Moments 1 c 1 63
62. nergy change actual value 0 2840E 07 threshold 0 1000E 05 geom gradient actual value 0 1547E 04 threshold 0 1000E 02 232 07657502709 Output 229 29031191903 potential energy 461 36688694612 Energy Moments Gradients 232 0765546194 dE dxyz 0 003181 232 0765749656 dE dxyz 0 000196 232 0765749995 dE dxyz 0 000198 232 0765750279 dE dxyz 0 000037 ff 232 0757937330 dE dxyz 0 018796 fas ts What next Start new job with current data as input Save as job template for further usage Manage Job s Important e Check the Status of the molecular orbitals and the status of the geometry optimization e In case that the orbitals MOs are not converged restart the job perhaps more SCF iterations or higher DIIS damping is required see Method section e If the geometry is not converged restart the optimization allowing more geometry cycles e Also make sure that the HOMO LUMO gap is positive Otherwise you have a hole in the occupation which might be what you want but usually this should not be the case and you did not get the proper ground state of the electronic structure Page 24 92 2 A quick tour TmoleX 4 0 TmoleXProject 2 6 Job Administration Ss EE File Edit Templates Results Extras Tools Help 7 fa A gt is ae H a Open 3D Molecular Buil
63. nononannnonncnnonannnonnnnncnnnnnnnnnannnnenannnns 70 Page 3 92 A o O ge nce letatalalalnn 11 6 1 Denne Jop templates lt td 71 02 1ADPIVJOD Templates natal la 12 0 02 RESUIES OT OD Template Sp aa 74 Balen process iaa Ao IS da cian 75 7 1 Read in and use several MOlCCUIES ccceccceececsececsecceeeeceuceneecesseeecseeseueeseaeessueecseeesseesaesenseesaeeass 75 Generate batch jobs from existing jODS o ccooococococncoconononocnnonanocononnnonnnnnnnnnnononnnonanononannnonannnnnnnnns 77 T2 ADOlY lemplates fOr DaIGh JOBS a eon en ADO DOS 78 7 2 RUN local OF FEIMOLEs Datel ODS ri peda 79 7 4 Visualize and export results Of batch jODS ccoonccccoccccoccccnnoconconcnonnncnnnonenononnncnncnnonnnnnnnnrnnnnnnnonannnos 83 MS A A A 84 Ot DO CUINILY ION cl ON at i5 tc dora a a E A arate A E a a a eas 84 BZ Add NEw remote AC NN stes rotatorios 85 ds tala Se mote OD eee een eee em er et ee ee Ere ee ies dede 87 8 4 Using a queuing system on a remote ClusSter oocccoccccncccnonccocncnconcncnnnnnoncnnnnnonnnnnoncnnonrnnonrnnnnrnnnnnnnnnos 88 COMBINA TE SUS ul aa e a rri 92 Page 4 92 1 Installation 1 Installation 1 1 Windows Prerequisites Windows Vista Windows 7 Windows 8 or Windows 10 The Windows version of TmoleX is distributed as a single executable file called TmoleX_ windows _ 4 1 exe To install TmoleX simply double click on TmoleX windows 4 1 exe and follow the installa
64. o the file basis_set_names txt which can be found in the TmoleX directory lt Install path gt COSMOlogic TmoleX15 TmoleX Page 17 92 2 A quick tour 2 5 3 Molecular start orbitals panel For any TURBOMOLE calculation an initial set of molecular orbitals is required This is done with an extended Huckel calculation in the Molecular Attributes panel If you do not yet have valid start orbitals the button will remain red Fie Edit Templates Results Extras Tools Help Eii 65 5 H 6 P open 3D Molecular Builder Jobs running local 0 4 remote 0 v E ProjectList Method S Statlob SF Results Y 5 TmolexProject i A E Mee EE Choose Job Template Charge Vv Apply Job Template ll Molecular Orbital Mar Orbitals gt Diagram Molecular charge o y Spin Sym Energy Hartree Degeneracy Occupancy HOMO LUMO Advanced settings AA A A AA Fermi settings Fermi Frozen orbitals for MP2 CC2 L Freezing point Hartree lt lt Previous Continue gt gt aa Oa n J x Perform an extended Hueckel calculation Symmetry If you click on Generate MOs a message box will come up aes Unpaired electrons EHT AOS E H ok cancel j Do not forget to set the molecular total charge before generating orbitals for IONS Click Ok The generation takes only a very short time to compute and the
65. ond Zoomfactor 100 Actual SMILES Draw your structure in JChemPaint and click on Get SMILES or Get SMILES and close to copy and paste the resulting SMILES of your painting into TmoleX and the 3D builder if open Detailed information about JChemPaint can be found on https jchempaint github io TmoleX 4 1 0 TmoleXProject File Edit Templates Results Extras Tools Help 7 D 565 EH 6 9 open a Molecular Builder Jobs running local 0 4 remote 0 15 11 AB System 0 0 17087 9 MB Choose Job Template ee Charge Use from input Apply Job Template AAA 25 Import Coordinate File 9 Open 3D Molecular Builder Jl A oran zo MIC OINC2C O NIC C O O C CHOISCI2 1M JJJ smies to 3D Units A v x Internal coordinates Help SE el Le lelalclel iwa ala SS Insert au Autodetect Symmetry Annhs Mow Daint Crain File View Edit Tools Display Type Window Help 500 scl tm AB im Cote TZ E El eel ci HJ Ou Nu Pal SE culer ul Rl Add Atom Or Change Element H CH N O 8 10 Hs implicit Zoomfactor 172 Actual SMILES O N1C C 0 O C CHCISCIAH YGetsmeS X Cose Wf GetSMILESanddose HE 0000 left mouse button Click or drag to select right mouse button rotate MMB move wheel zoom Page 32 92 3 T
66. outline of the procedure used by TmoleX to access to remote systems e ssh and scp are used to start jobs and to copy the files from one system to another We use a locally modified version of PuTTY http www chiark greenend org uk sgtatham putty PuTTY is copyright 1997 2009 Simon Tatham Portions copyright Robert de Bath Joris van Rantwijk Delian Delchev Andreas Schultz Jeroen Massar Wez Furlong Nicolas Barry Justin Bradford Ben Harris Malcolm Smith Ahmad Khalifa Markus Kuhn Colin Watson and CORE SDI S A Permission is hereby granted free of charge to any person obtaining a copy of this software and associated documentation files the Software to deal in the Software without restriction including without limitation the rights to use copy modify merge publish distribute sublicense and or sell copies of the Software and to permit persons to whom the Software is furnished to do so subject to the following conditions The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software THE SOFTWARE IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT INNO EVENT SHALL SIMON TATHAM BE LIABLE FOR ANY CLAIM DAMAGES OR OTHER LIABILITY WHETHER IN AN ACTION OF CONTRACT TORT OR OTHERWISE ARISING FROM OUT OF OR IN CONNECTION WITH
67. pace for the calculation If and how important those settings are depends on the method and job type For ground state single point energies and geometry optimizations at Hartree Fock or DFT level neither more memory nor more disk space will speed up the calculation significantly For vibrational frequencies IR and Raman spectra post Hartree Fock methods or excited state calculations more memory can improve efficiency a lot Please note that the given memory value is not the total amount of RAM the program will use just the parts that can be adjusted Hence do not enter more than roughly 80 of your total memory here to avoid huge performance problems Page 23 92 2 A quick tour 25 6 Results Whenever a calculation is finished you can find a summary in Results The output files and a viewer see next chapter can be opened from here File Edit Templates Results Extras Tools Help D D a fs 82 Open 30 Molecular Builder J J Memory used for_Tmolex HAS 4 5E K_ _ _ __ z __ Sn Y E TmoleXProject F COPPA LO LOST EES ROEDER OT LEO LEOPOLDO DOO LLL O ODED DOOD OLE L DOLE LODE LOTT TELE LOTTE ae Choose Job Template wv Charge Use from input w Apply Job Template SSS ae eo Type of Calculation Geometry Optimization Status mos Converged SCF Convergence Open View HOMO LUMO gap 5 139 eV Status geometry Converged Convergence Geometry Convergence Criteria Sconvinfo e
68. propylamine Molecule Number of atoms Charge Multiplicity Energy Dipole moment Zero point vi _ Y aniline TmoleXProject_methylamine 7 0 0 Singlet 95 774187 1 392422 J job_BATCH_17 TmoleXProject_ethylamine 10 0 0 Singlet 135 062169 1 351271 gt 7 TmolexProject_m TmoleXProject_propylamine 16 0 0 Singlet 213 629261 0 825862 gt 3 TmoleXProject_el l TmoleXProject_aniline 14 0 0 Singlet 287 413943 2 052376 gt TmolexProject_p 9 gt TmolexProject_al 3 job_GEO_18 esult Job Comparison Results Multiple Jobs Comparison Movie Freeze None lt y vV Y The resulting table can be saved as spread sheet The Export Files button allows to save COSMO energy or coordinates files of different format Save Save In Tmolex E cosmo COSMO files energy geo files E Geometry files xyz sdf ml2 pdb C Users Tmolex Documents Tmolex xyz geometry files COSMO and energy files are usually only needed for the COSMOtherm program TmoleX will save all files of the given type to the chosen directory Page 83 92 8 Remote jobs 8 Remote jobs TmoleX as well as the client version of TmoleX which is freely available from COSMOlogic web site is able to start jobs on remote Linux Unix machines using a secure shell 8 1 Security information To determine if you do want to use this feature and worry about security here is a short
69. ptimization with small basis set frequency analysis geometry optimization with larger basis set CD UV Vis spectra at DFT level single point energy calculation with post Hartree Fock method The template will have to be named when saving and can be found in the pull down menu afterwards 6 2 Apply job templates To use a template just choose a saved template from either the template tool bar Choose Job Template Charge Use from input Apply Job Template or from the menu Templates TmoleX will alter the settings accordingly generate start orbitals and brings you directly to the start job panel The molecular charge can be either those of the template if the Charge pull down menu is let empty or whatever the user chooses in the tool bar Generate a new job read in or build a molecule Then select a template set the charge or use the default and click on 4Pply Job Template TmoleX will prepare the input and jump to the start job panel job 1 job 2 Use resources OPT FREQ xml Memory used for 500 0 MB Job Name Jobi Job2 Symmetry check on on Disk 0 MB for HF Basis functions def SV P def SV P No of CPUs 1 Charge used from input used from input Multiplicity Automatic RHF UHF Automatic RHF UHF X ii ia i ai Freeze off off Level of theory DFT Disp DFT D3 BJ damping Grimme et al 2011 b p DFT Disp DFT D3 BJ damping G Cosmo off off Job Type GEO FREQ Save and Run Run local Save
70. re are several web sites which provide SMILES code for a large number of structures like ChemSpider http Awww chemspider com If you have a SMILES code there are two ways to add it to the 3D builder 1 directly in TmoleX in the geometry part of the input generation just add the SMILES code to the field shown below and click on PH suies to3o ii Import Coordinate Fle 82 Open sDMoleciarBuider Moran Y Enter or paste your SMILES here ts Ay 2 orin the Builder if the Molecules section is selected add it to the SMILES field and click on the button Molecules Atoms Y 4 Molecule gt iy alcohols lie dl amino_acids li de carbonyls gt i hydrocarbons gt al misc ho del pah ai de rings lo dal small_common The difference is that clicking on the WP sues to 30 in TmoleX will replace whatever you already had as structure in the Builder while adding SMILES to the Builder itself will act as adding one of the fragments or structures of the fragment library The SMILES to 3D conversion is done using RDKit http www rdkit org Page 31 92 3 The 3D visualization 3 4 The 2D Builder If you start the 2D builder click on AP raw D to open a new window of JChemPaint File Edit View Atom Bond Tools R groups Templates Help E lem gt 1 I aA Ga al AN aa v Insert Draw B
71. right mouse menu To add or remove labels for several atoms or bonds just select several items and then use the right mouse button for the selection Bond Atom Style gt Edit additional label 7 Nu O er Select bond partners Qi Additional Substitute with b Change element r Coordinate gt o As connecting atom Arrange Saturate e Measures can be added with the right mouse menu what is measured depends on what you have selected o select two atoms measure distance Bond Atom Style Labels Edit additional label Translate Rotate Create bond Merge overlapping atoms Add atom at center Create group Page 48 92 3 The 3D visualization select two bonds measure angle Bond Atom Style Labels Edit additional label Translate Rotate Scale Scan freeze bond angle Change bond angle Swap bonds o select three bonds measure torsion Measures can be selected and deleted with the Measures pull down list Objects Measure 3 87A T Measure Measure 3 87A z Delete Page 49 92 3 The 3D visualization 3 10 Moving Rotating Scaling It is often helpful to move or rotate parts of the molecule to a new position This can be done within TmoleX with several powerful possibilities but the usage is not self explaining So here are the options e Select several atoms hold shift key and select the atom around which the rotation shall be done The last atom that is
72. rmats which contain multiple structures like sdf Multiple selections within the file browser are of course also possible Page 75 92 7 Batch processing F 4 TmoleX 4 0 TmoleXProject Ss e es File Edit Templates Results Extras Tools Help 3 fa ASAS EH Ga 9 Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmokx __196 8 270 2 MB System 0 0 6296 2 MB v E ProjectList Atomic Attributes y Molecular Attributes Method P Startlob F Results Y Gs TmolexProject y A a i Y job_GEO_1 Choose Job Template y Charge w Apply Job Template CE Y job_GEO_5 oo sta gultiple Coordinates Y job_SP_6 AE hiia Y job_SP_7 Y job_SP_8 2 add Molecule 52 Delete Molecule gt 7 job_SCAN_9 Sumber Ay gt 7 job_SCAN_11 gt job_TEMPLATE_14 job_notRun_15 methylamine ethylamine Lookin Test cases L cosmo files A out_10 xyz A out_3 xyz A out_11 xyz CA out_4 xyz A BigCluster2 xyz A out_12 xyz A out_5 xyz EC_25112007 sdf out_13 xyz A out_6 xyz irgendeines cosmo out_14 xyz A out_7 xyz job_BATCH_33 cosmo out_15 xyz A out_8 xyz job_BATCH_33 energy out_16 xyz A out_9 xyz A leflunomide_1 xyz out_17 xyz test cml A out_0 xyz A out_18 xyz A out_1 xyz A out_2 xyz File Name amines sdf Files of Type all coordinate files Apply Job Tgfiplate
73. s COSMOlogicAppData Ja Saved Games L COSMOlogicAppDatal1 Searches cosmothermx12 MA Desktop E Documents La Downloads LE Favorites File Name C Users Tmolex TmolexProject Files of Type The default directory is called TmoleXProject in your home folder Just click on Select to accept the default or generate a new directory and choose this one You are now ready to perform your first Turbomole job Fie Edit Templates Results Extras Tools Help 1h S Open 3D Molecular Builder Jobs running local 0 8 remote 0 Memory used for TmoleX System 0 0 17087 9 MB D a amy 8 aa v E Projecttist Y 35 TmolexProject B job_notRun_1 Coords amp Sym 25 Import Coordinate File 82 open 3D Molecular Bulder A Dran D Atomic Symmetry DY sms to3D Units Aw Internal coordinates Number of atoms 0 Current point group cl Max tolerance 0 001 U Autodetect Symmetry New Atom New point group ci Apply New Point Group _ Delete Selected Atoms Number Element x Constrai Value Start End Stepsize Page 10 92 2 A quick tour 2 2 An illustrative example Part 1 This section will guide you through the process of performing a DFT energy calculation and a ground state geometry optimization of a molecule for which input coordinates exist e g benzene Open Coordinate File Look In rings E benzene sdf 14 benzimidazole sdf
74. s are of course added by TmoleX automatically Parallel settings TURBOMOLE contains two different parallelization schemes SMP runs almost all jobs in parallel on a multi core multi CPU or NUMA system MPI on the other hand is able to utilize several different nodes for one job but the number of parallelized modules is smaller than in the SMP version TmoleX by default sets SMP for parallel remote jobs which are submitted to a remote system without using the queuing system option and MPI whenever the queuing system option is activated The number of total CPUs is also set automatically In some cases a queuing system requires different settings than TmoleX applies by default The two options LJ add PARA_ARCH SMP MPI E add PARNODES number of CPUs help to overwrite those defaults If you uncheck one of the two or both options make sure to add the environment variables PARA_ARCH and PARNODES by hand if needed Note that you have to tell your queuing system about the number of CPUs you want to use PBS SGE PBS l select 4 ncpus 8 5 pe mpi 32 The default in PBS is to set the number of nodes with select and the number of CPUs per node by ncpus In this example 4 nodes with a total number of 32 CPUs will be used So set PARNODES to 32 For SGE like queuing systems one has to tell SGE which parallel environment pe one wants to use The name for the PE depends on your local SGE installation so please check existing SGE su
75. t multtiple selected gt Bond properties Type single ail Length A 14312 Guess Length Guess Dihedral Angle G Pa C Freeze Bond Angle Scan Bond Angle Measure Bond Atom Style Labels Edit additional label Invert selection Measure bond angle Translate Molecules Atoms Y 4 Molecule Rotate y Y alcohols e 1 butanol sdf Scan freeze bond angle 2 propenol sdf ethanol sdf Change bond angle gt geraniol sdf lt isopropanol sdf Cans Both onal ccf The properties of the angle are shown and can either be changed by clicking on the left mouse button and dragging the mouse or by editing the field Like for torsional angles the small and big fragment option decides which part of the molecule is being moved TmoleXProject job_notRun_3 Number of atoms 9 Number of bonds 8 Objects multiple selected gt Change bond angle Angle 117 538 O small fragment big fragment A Ree Nr Molecules Atoms v Molecule Y 1 alcohols J 1 butanol sdf Page 43 92 3 The 3D visualization 3 7 1 Building step by step 2 Instead of changing an atom to a different element to change hybridisation and use the saturate option an atom can also be replaced by a pre stored fragment GM TmoleXProject job_notRun_3 x Number of atoms 9 b Z Objects Atom H 7 A
76. tains two lines e the first one represents the number of the atom which will be replaced when using the Substitute with option in the right mouse panel see below e the second line can contain the name of the fragment the way it will be displayed in the Molecules section of the builder Page 29 92 3 The 3D visualization The replacement atom can be chosen with the right mouse button menu Bond Atom Style Label Edit additional label Select bond partners Substitute with Change element d Coordinate Arrange Saturate The File Save to Fragment directory menu can be used to store the structure that is visualized in the 3D window to the users data base The atom that is selected when saving is the one that will be replaced 3 2 Import structure Instead of building a molecule from scratch an existing molecule in different formats sdf ml2 xyz cosmo can be imported using the File Open menu entry within the visualizer alia LI File View Edit Tools Display Type i Save Export Coordinates Save to Fragment Directory Save Changes and Close This structure can then be used for modification or being saved in the user data base as described above Page 30 92 3 The 3D visualization 3 3 Use SMILES code Most organic compounds can be described with the SMILES notation see https en wikipedia org wiki Simplified_molecular input_line entry_system and the
77. that the file has execute permissions chmod a rx TmoleX_linux_4 1 sh before starting it then follow the instructions on screen The full version of TURBOMOLE 7 0 is included in the TmoleX package Features that are not supported by TmoleX can be used by the command line version After the installation of TmoleX TURBOMOLE can be used from the command line as usual Just set STURBODIR to the TURBOMOLE directory of the TmoleX installation and extend the PATH to STURBODIR scripts and STURBODIR bin sysname the binary directory Or alternatively a shell can be started by TmoleX with the correct settings by using the right mouse menu in the project list see below Page 6 92 1 Installation 1 3 Mac OS Prerequisites Mac OS X 10 6 and newer The Mac OS version of TmoleX is distributed as a single file called TmoleX_macos 4 1 dmg To install TmoleX simply double click on TmoleX_macos_4 1 and follow the installation instructions After installation TmoleX is available in the chosen folder by default in Application COSMOlogic Tmolex14 Features that are not supported by TmoleX can be used by the command line version After the installation of TmoleX TURBOMOLE can be used from the command line as usual Just set STURBODIR to the TURBOMOLE directory of the TmoleX installation and extend the PATH to STURBODIR scripts and STURBODIR bin sysname the binary directory Page 7 92 1 Installation 1 4 On
78. them free for being utilized by TmoleX and your operating system When starting the job just set the number of CPUs in the Start job panel directly Use resources Memory used for 500 0 MB Disk 0 MB for HF No of CPUs f Delete scratch files after run Page 80 92 7 Batch processing Using many cores or CPUs remote systems Similar to the local system settings you can also set the number of CPUs on remote systems using the Extra menu File Edit Templates Results Extras Tools Help Settings Remote Systems k this will open G Add new Machine 4 Save Machine 4 Save Machine as Ell Import Machine Ef Export Machine Note runs only on Linux Unix systems Machine IP Group Name User Work directory TURBOMOLE direc Use CPU Utilized CPUs RAM MB Queue Y SGE duster gt enzo4duster duster SGE duster n394 scrfen394 fusrfapp TURBO 1 0 0 a E E n tmolex linux14 Inuxi4 Default tmolex fromefimol fsoftware TURBO 1 0 o gp aes tmolex 10 0 0 208 10 0 0 208 Default tmolex home tmol software TURBO 1 0 0 D tmolex 10 0 0 208 There is the entry e Use CPU the total number of CPUs TmoleX is allowed to run on that system for all jobs The default is 1 which is equivalent to unlimited G Add new Machine 4 Save Machine 4 Save Machine as Ell Import Machine Elf Export Machine Note runs only on Linux Unix systems MEET
79. tion instructions After installation TmoleX is available in your Windows Start Menu or as an icon on your desktop Please Note TURBOMOLE 7 0 for Windows is included in the TmoleX package You will not have to install it additionally Some features of TURBOMOLE that are based on classical Unix scripts are not yet ported to Windows O Numerical second derivatives script NumForce O automatic BSSE calculations program jobbsse The TURBOMOLE version for Windows 32bit includes one generic type of serial 32 bit executable only without special optimization for a certain type of CPU It runs on any processor that is compatible to the Pentium 4 instruction set which supports SSE2 The 32bit Windows version is not recommended for methods and jobs that require a lot of memory or CPU time like coupled cluster calculations We recommend either the 64bit Windows version or the quantum chemists work horse Linux 64bit The TURBOMOLE version for Windows 64bit includes serial and parallel 64 bit executables IBM s Platform MPI Community Edition is included in the installer parallel jobs should run out of the box but you have to take care that the Windows firewall allows the processes to communicate with each other Page 5 92 1 Installation 1 2 Linux Prerequisites Linux distribution based on Kernel 2 6 x and newer The Linux version of TmoleX is distributed as a single file called TmoleX linux_4 1 sh Please make sure
80. tom rties Bond Atom Style cis Label Element H Edit additional label x 5 ES Translate y gt Select bond partners Z Fa Substitute with alcohols gt Charge Change element gt amino_acids Hybridisation custom Coordinate gt carbonyls gt Saturate Ar Arrange misc gt Saturate pah gt Paste rings gt Molecules Atoms copy Molecules atoms Y Molecule Cut Delete Y 1 alcohols q 1 butanol sdf 2 propenol sdf Attach n h custom atom Open to edit sdf Mi methanol sdf tert butanol sd gt de amino_acids Select an atom use the right mouse button and click on Substitute with Note The fragments that are shown are the molecules of the user data base or the default pre stored molecules after installation as shown here When choosing Attach the connecting atom which was marked as such when saving the structure to your fragment data base will directly be substituted The builder will automatically switch to the dihedral mode Use the left mouse button to rotate around the new bond To get back to the selection mode double click on the background hit the Esc key or use the Li button Page 44 92 3 The 3D visualization Alternatively any other atom can be used as connecting atom Atom properties Bond Atom Style Labhd gt Element H Edit additional label x 1 116 Translate Y 0 394 Select bond partners Z 1 286 Subst
81. tras Tools Help N D a a E 6 P open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 128 1 200 9MB System 0 0 6296 2 MB v E ProjectList h Y 5 TmolexProject t Y job_GEO_1 Choose Job Template w Charge 7 ly Job Template Y job_GEO_5 Y Job Results Type of Calculation Single Point Calculation Status mos Converged Open Viewer HOMO LUMO gap 5 139 eV BS Orbital Density Plot Status geometry Not performed Convergence Gradients Energy Vibrations zero point VIBRATIONAL energy 0 0978161 Hartree Thermochemical j SCF energy 232 0765750 SCF E vib0 231 9787589 Population Properties NMR Shieldings View cosmo File Open Files e cc Vibrational Modes PPP AA Vibrational Spectrum 5 Moments mode metry wavenumber IR intensity selection rules ci cm 1 km IR Raman las UV Vis Spectrum gt ree ero E ls CD Spectrum a ees ie a BB Raman Spectrum 5 0 00 0 00000 gt 6 0 00 0 00000 Oo E 7 a 401 73 0 00002 YES YES What next 8 a 402 48 0 00008 YES YES 9 a 600 69 0 00000 YES YES Start new job with current data as i 10 a 600 72 0 00000 YES YES 11 a 670 28 87 98540 YES YES Save as job template for further us 12 a 712 74 0 00000 YES YES 13 a 837 52 0 00000 MESES ss anon mn mmm m m v L lt lt Previous OS a ape A Select a specific mode and click play TmoleXProject job_SP_16 vibrations X 4 Number of atoms 28 Number of bonds 29 frequen IR inten 0 00 0 00000 33
82. ts Extras Tools Help 115656 EH 65 9 open 30 Molecular Buide Jobsrunning local 0 8 Memory used for TmoleX 60 6 84 5MB System 0 0 17087 9 MB Y Bil Projectist Geome Atomic Attributes Molecular Attributes Start Job Y E TmolexProject B job_notRun_1 Chsese Job Template v Charge Use from input w Apply Job Template Start Calculation Job type DFT Functional b p Geometry Offflation Ground state Spectra 8 Excited States P MERA he Single Point gt UV Vis and CD vertical excitations NMR shieldings Basis set def Sv P Symmetry C1 ingle Point Properties Raman amp vibrational frequencies Convergence Parameter Potential Energy Scan PES Optical rotations dynamic polarizability Eneray Static polarizability 10 Density Transition State Search gt Templates gt Batch processing gt Use resources Memory used for Options Me Disk 0 Convergence criteria Energy 6 101 Hartree No of CPUs 1 Gradient norm 3 dE dxyz 107 Hartree Bohr FJ Delete scratch files after run Max no of cydes 50 Use internal redundant coordinates Save and Run Depending on the job type different options for the chosen job are displayed in the Options section The Method section briefly summarizes the settings done in the four menus before method symmetry basis set etc Finally the Use resources part can be used to set maximum amount of memory RAM and disk s
83. ua pa Si cir Sz ST GI AIAIALAL ATA po pr pr pa pa pa o a da 0 0 0 S Basis for individual Atoms Select items from table or graphic viewer Choose Basis Sets The basis set is def SV P by default for all atoms You have the possibility to select one basis for all atoms basis sets for given elements or basis sets for individual selected atoms Hint If you are not familiar with the modern Karlsruhe Ahlrichs type basis sets but with old Pople type basis sets only 6 31G is of similar quality than def SV P 6 31G def SVP and 6 311G ae def TZVP Page 16 92 2 A quick tour The drop down selection Basis Set for all Atoms contains just the Karlsruhe family of basis sets since those are available throughout the periodic table Basis Functions 102 Basis Set for all Atoms defsvP T def2 Sv P def2 5VP def2 TZVP def2 TZWPP def2QZWP def2QOZWPP def2 SVPD def2 TZWPD For heavy elements a basis set which is optimized for two component ECPs and two component calculations dhf SV P 2c dhf SvP 2c look at the automatically loaded ECPs dhFTZVPP 2c by clicking on dhf QzvP 2c dhf QZvPP 2c Selecting one of those will enable the relativistic Two component treatment options in the Method section later on NOTE If you miss some basis sets which are present in the basis set library or if you have added own basis sets to the basis set library add them t
84. ualization LUMO 3 J LUMO 2 LUMO 1 LUMO HOMO HOMO 1 HOMO 2 HOMO 3 HOMO 4 m 1 15 a a _ O o a O a O Y LE E amp 0000 left mouse button Click or drag to select right mouse button rotate MMB move wheel zoom Page 58 92 3 The 3D visualization There are a lot of options and possibilities when visualizing 3D surfaces The most important things are e while it can be annoying that the full 3D grid is being calculated which can be very time consuming TmoleX can now use this data to generate the 2D surface for a given iso value on the fly Use the slider or the field for the iso value to change the threshold e The Display options are O O isosurface use one iso value to plot the surface at this value cloud plot each point of the 3D grid which is within the Min and Max value The colours of the points depend on the Min Max range Isoplot plot a plane or an arbitrary surface which can be given as implicit equation like x 2 y 2 z 2 4 Avoid blanks and let the mouse pointer rest over the field to get some help coloured with the value of the chosen property Colour depends on the Min Max range lf you see nothing not enough or not enough colours change Min and or Max value Isoplot again click on isosurface and a file chooser will open Click on e g td plt total density and set an iso value below
85. ul option is to merge overlapping atoms a read in two benzene b move one fragment close to the second one This can be done in two ways i select one of the two benzene by double clicking on one atom and then select the translate tool or hit w on the keyboard Hold left mouse button and move the fragments such that they overlap switch to another direction and or use the along view button to move in the direction of the monitor system of coordinates Around View J PivotatCOM_ a Leal E View Page 35 92 3 The 3D visualization li create a bond between two atoms select it and change its length to zero UA rr Bond Atom Style Labels E Edit additional label y enserio O Translate gt l Rotate Scale gt e US Merge overlapping atoms Add atom at center Create group 111 and even easier Select two bonds of the two benzene rings and select Merge bonds The moved fragment should look like this The zero bond length method leads to Page 36 92 3 The 3D visualization Double click on the background or hit the Esc key or use the left mouse button to get to selection mode Draw a box around the overlapping part and select Merge overlapping atoms from the right mouse button menu Bond Atom Style Labels Edit additional label Invert selection Translate Rotate Scale Ring conformation Add atom at clatter Create group Cut Delete All atoms
86. which have a little bit of overlap will be joined in a way that the lighter atoms is being deleted Page 37 92 3 The 3D visualization The trick to set a bond length to zero works only in cases where the selected bond is not part of a ring Page 38 92 3 The 3D visualization 3 6 1 Building step by step 1 Change to selection mode q or ESC key or arrow button on the left side if you are not already in this mode Select an atom TmoleXProject job_notRun_3 Number of atoms 6 Number of bomds 5 b Objects Atom H 4 1 127 5 A 0 5252 0 8982 A Charge Hybridisation custom v Saturate Arrange pekte Molecules Atoms Y J Molecule Y alcohols 1 butanol sdf 1 2 propenol sdf ll atharel edt On the right side the properties of the selected item atom bond measure etc are shown For objects which are hard to select with the mouse the Objects chooser can help since it contains all displayed objects including measurements and constraints Atom properties Element H z Edit x 1 127 A y 0 5252 z 0 8982 Charge o Hybridisation custom Saturate Arrange nea A Most entries can be changed in the fields Page 39 92 3 The 3D visualization Change the Element from H to C and also the Hybridisation to sp3 tetrahedral F Objects Atom C 4 Y Atom properties Element fe v Edit x 1 1272 A
87. y 0 5254 z 0 898 Charge ps tn i a Saturate one bond sp linear sp2 trigonal Molecules At sp2 lone pair Y Molecule SP3 lone pair Y J alcohols EXEMGUEL G gt 1 but sp3d trigonal bipyramidal L 2 10 sp3d2 octahedral M TA Next click on Saturate to add missing hydrogens to the selected atom according to the given hybridisation Page 40 92 3 The 3D visualization 3 6 2 Change bond length Now the bond length to the newly created methyl group is set to a default single bonded C C lenght but can be changed by selecting the bond Either enter a new value or let TmoleX guess the length according to vdW radii Objects Bond Atom 1 Atom CQ 1 pe Bond properties Type single z Length o 1 542 Guess Length Guess Dihedral Angle C Freez Length Scan Length LJ Freeze Torsion Scan Torsion The length and also many other things can be done by using the context menu of the right mouse button Hint If you want to change a bond length or an angle or torsion and there are no bonds to select simply add a new bond between two selected atoms using the right mouse menu Bond Atom Style b Label gt Edit additional label Measure torsion Scan freeze length Scan freeze torsion S Guess dihedral angle a Change torsion Add atom at center Delete Page 41 92 3 The 3D visualization

TmoleX User Guide

Contents

Download Pdf Manuals

Related Search

Related Contents