TmoleX
Contents
1. tio TmoleX visualiza o0 x File View Tools Window Help ME DO ALA Fra Objects Bond 1 43 lo F TmoleXProject job 2 Bond prope Type sinale v Length A 1 0974 Guess len i Guess dihedral angle Scan freeze length Scan freeze torsion Molecules Atoms 7 Molecule a c alcohols tI D 1 butanol xyz C ethanol xyz D isopropanol xyz EY methanolxyz a tert butanol xyz J aromatics D benzene xyz EJ carbonyls a carboxylicacid xyz D formaldehyd xyz 4 Save as Molecule Delete Molecule LMB Click or drag to select RMB rotate MMB move wheel zoom Edit additional label Guess length Guess dihedral angle d Change torsion Measure torsion Scan freeze length Scanifreeze torsion 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 Page 29 64 3 The 3D visualization 3 1 6 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 Label b Edit additional label Guess length Guess dihedral angle Change torsion Measure torsion PON Ss 0 ala2. Scan freeze torsion fete The torsion around which the molecule will be rotated is being shown Use the left mouse button to change the Scan freeze length 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 hange bond angle Angle 9 952 e small fragment big fragment Molecules Atoms C3 Molecule a J alcohols 3 E 1 butanol xyz E ethanol xyz Ey isopropanol xyz Y methanolxyz Y tert butanol xyz ci aromatics D benzene xyz A narhamar At Page 30 64 3 The 3D visualization 3 1 7 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 Objects lt muttiple selected gt h Bond properties fi o Fs type singled Length A B 14314 M cues dhesratanie Measure acanfreeze bond angle e y Labels Molecules Atoms oF Edit additional label 3 Molecule la 5 Invert selection 7 4 1 butanol xyz B ethanol xyz 4 isopropanol xyz ae 4 methanol xyz 4 tert butanal xyz Measure bond angle GJ aromatics Scani
3. 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 o Holding the left mouse 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 not 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 Page 38 64 3 The 3D visualization e Finally the scale tool key r scales or resizes relative distances between atoms Add a benzene ring select it and use this tool to see what it does 3 5 The gradient viewer Once you have completed a geometry optimization you can open the gradient viewer from the results panel 4 Tmolex 3 0 moe roae o ovo File Edit Templates Help DG a2 BE By By pateurremmates v userremmates azarosa MA Project Geometry _Atomicambutes _Moteculararributes _memod _stamob Results By Tm
4. wows non ef WN e e Po H N You can look at the mode in the 3D visualization Select a specific mode and click play Page 47 64 4 Properties eno IN view Tools Window Help a A E FI Gradients vibrational Modes Ie Internal coordinates P Builder e Orbital Viewer Temperature sets the amplitude TmoleXProject job 2 ibrations Use the play buttons and or the slider to see the mode vibration Temperature 298 a g a a a He an a ol 0 0 0100 Rotate the molecule Page 48 64 4 Properties 4 2 IR spectrum Use the to open the IR spectrum 401 72 ax freq 3116 12 Frequency shitt bo Sampling points j900 Broadened by Gaussians Line spectra E o 2 o ES d i 500 1000 1500 2000 2500 3000 frequency Standard deviation for the broadening Gaussians 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 49 64 4 Properties 4 3 Nuclear magnetic shielding For the calculation of nuclear shieldings choose this job type and simply run it Job type Geometry Optimization O Ground state Spectra amp Excited States Y I
5. RAMAN Spectrum IR Spectrum NMR Shieldings Copy and paste the values to a spread sheet for further usage Note that to get the NMR shifts you have to do a calculation also on the reference molecule like TMS for carbon with the same method and basis set Page 50 64 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 select singlet or triplet the number of excitations and run it Job type beometry Optimization O pectra amp Excited States 4 IR amp vibrational frequencies me he ane rn Sees ic ale Sei WW AMU LL YEL 2XCMa tons NMR shieldings Raman amp vibrational frequencies Potential Energy Scan PES Wa Optical rotations dynamic polarizability Static polarizability File Edit Templates Help ela a y Derou Tempiates gt fusertempines azotan FB Projecttist Geometry Atomic Attributes _ Molecular Attributes _Method _startJob Results 83 TmolexProject Job Results Job Comparison y job_GEO_1 y job_SP 7 Type of Calculation Single Point Calculation Status Mos Converged Y job_GEO 8 HOMO LUMO gap 6 008 ev y job_SP_9 Status Geometry Not Performed y job_SP_10 Energy Open Viewer 210 2055177762 3587307323 418 5642485085 210 2109912746 2552831
6. panel If you do not yet have valid start orbitals the button will remain red ProjectList 7 Bs TmolexProject a job_notRun_1 File Edit Templates Help Start Job Results XN 5 ae Spin Symmet Energy Hartree Degenera Occupancy Molecular charge boo Multiplicity Automatic Automatic RHF UHF gt Frozen orbitals for MP2 CC2 C Freezing point Hartree 5 Perform an extended Hueckel calculation Symmetry c1 If you click on Generate MOs a message box will come up Charge 0 Unpaired electrons 0 0 EHT AOs H 3P DZ 2S DZ Do not forget to set the molecular total charge before generating orbitals for IONS Page 14 64 2 A quick tour Click Ok The generation takes only a very short time to compute and the initial molecular orbital are displayed File Edit Templates Help mos Geometry Atomic Attributes metnod Esama ress Bs TmolexProject Molecular Orbital Job_notrun_1 Molecular orbitals Molecular charge g erovlHa ocupan Multiplicity restricted Fully occupied Partly occupied Delete MOs Advanced Settings Fermi Settings C Fermi Frozen orbitals for MP2 CC C Freezing point Hartree a AE a 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
7. ethanol xyz 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 Objects AtomH 3 ly Atom properties x 1 106 4 y 1 015 A 2 O a Charge Most entries can be changed in the fields Page 27 64 3 The 3D visualization Change the Element from H to C and also the Hybridisation to sp3 File View Tools Window Help wim 0 Al er X A TmoleXProject job 2 a A Atom properties Element c v a 7 a 1 106 A a 1 015 A oA Charge to Hybridisation custom lv amp Saturate a EDO ii sp3 tetrahedral EJ Molecule sp3d trigonal bipyramidal C alcohols sp3d2 octahedral D 1 butasp3d3 pentagonal bipyramidal D ethan Sp3d4 twisted cube isopropanol xyz Y methanolagz D tert butanol xyz EJ aromatics i 1 i Save as Molecule Delete Molecule J E Next click on to add missing hydrogens to the selected atom according to the given hybridisation Page 28 64 3 The 3D visualization 3 1 5 Change bond length Now the bond length to the newly created methyl group is too short so select the bond and either enter a new value or let TmoleX guess the length according to vdW radii
8. PBS it l nodes 1 Export environment PBS cd PBS O WORKDIR This is a PBS 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 not give a 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 Page 63 64 7 Remote jobs PBS cd PBS O WORKDIR 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 4 TURBODIR is being set by TmoleX so you do not have to enter it again here 5 The commands to start the TURBOMOLE jobs are of course added by TmoleX automatically Page 64 64
9. ojoo N DD MAN T T T T TIT O O O O O O DODOODOOODOTI ojojojojojojojojojojolo OOL Continue gt gt Page 12 64 2 A quick tour 2 5 2 Basis set panel The basis set is being defined in the Atomic Attributes panel File Edit Templates Help Dojo a gt a ProjectList tribut Start Job Results 9 Bs TmolexProject Basis Functions 102 Basis set Nuclear charg En Basis Set for all Atoms def SV P 12 011 15 job_notRun_1 aer HR defsviP sw 3 NA azar ff geese naa fg o de A tt del af 2 Basis for elements C def SV P Ba 4 C EA C H aesvi sd 3 H gt 0 H gt on H je 12 H jd Basis for individuel 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 marked atoms Hint If you are not familiar with the modern 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 def TZVP Page 13 64 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 __
10. Objects Constraint stre C6 N9 To delete constraints select here and delete Delete gt Constraints Constraint stre C6 N9 Constraint To scan along the coordinate activate the CI Mark forscan lt check box and set minimum maximum and the step width not the number of steps Minimum Maximum Step size Page 52 64 5 1 Defining fixed internal coordinates e Select two adjacent bonds click on the right mouse button and use the Scan freeze bond angle option Labels Edit additional label a gt Fimvertscecion MS Translate Rotate Scale Change bond angle measure bond angle supone 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 Labels a Edit additional label Invert selection Translate 9 8 Wee Rotate Scale Change torsion Measure torsion Scan freeze torsion Delete a Page 53 64 5 2 Use internal coordinates 5 2 Use internal coordinates TmoleX will automatically generate a list of internal redundant coordinates if you accept t
11. 15d The MOPAC7 button will open a new window with several options a Am1 cosmo pma MNDO Geometry optimization optimization Transition state search C UHF Charge lo Read restrictions start calculation 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 33 64 3 The 3D visualization 3 3 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 Show label Show background Style C Number Symbol Charge _ Additional Bonds Show label t Show background 4 Style Length Additional 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 b
12. Default Templates M User Templates M 101 1128 7 mB Results Show this Job Close this Job Stop this job View Job directory Delete this Job The output of the status command is shown directly underneath the job list 3 Script to start Job enter here ID Name Type Start Sto Machine 1 ob_GEO_1 GEO DFT RI B P charge 0 c1 def SV P O May 28 2010 11 32 0 May 28 2010 11 32 2 Local 7 ob_SP_7 SP DFT RI B P charge 0 c1 def SV P FREQ Jun 1 2010 10 49 24 Jun 1 2010 10 51 55 Local 8 GEO DFT RI B P charge 0 c1 def SV P O Jun 1 2010 10 58 28 Jun 1 2010 10 59 23 Local 9 SP DFT RI B P charge 0 c1 def SV P NMR Jun 2 2010 12 00 07 Jun 2 2010 12 00 12 Local 10 SP DFT RI B P charge 0 c1 def SV P EX Jun 2 2010 12 03 23 Jun 2 2010 12 03 31 Local 14 SP DFT RI B P charge 0 c1 def SV P ON Jun 2 2010 11 19 26 Jun 2 2010 11 20 33 10 0 0 250 15 SP DFT RI B P charge 0 c1 def SV P Jun 2 2010 11 20 32 Jun 2 2010 11 21 39 10 0 0 250 17 job_ i GEO DFT RI B P charge 0 C1 def SV P O Jun 2 2010 11 27 45 Jun 2 2010 11 29 51 Local 18 ljobGEO 18 OO tore harge 0 1 def SV P 0 This is the field where a usual script that is used to submit jobs to a queue can be entered Example Name of your run FPBS N TmoleX job tNumber Of nodes to run on
13. 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 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 ta or press the key w Hints o 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 37 64 3 The 3D visualization File View Tools Window Help we O A Pie ir a Y Gradients Y F along view Molecules i isobutane xyz i methane xyz i propane xyz e misc B anthracene xyz E azulene xyz Cy chO xyz i ferrocene xyz B h 20 xyz B indole xyz i naphthalene xyz e dd EA omh wrr BE a Save as Molecule Delete Molecule J LME Click a handle and drag to translate the selection RMB rotate MME move wheel zoom
14. 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 when using the Substitute with option in the right mouse panel see below Page 25 64 3 The 3D visualization 3 1 3 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 te File View Tools Window Help SavelExport coordinates Save changes and close This structure can then be used for modification or being saved in the user data base as described above Another possibility is to load two or more molecules and select one atom of two different fragments Labels Edit additional label Invert selection Translate Rotate Scale Measure distance Create bond Create group Delete 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 26 64 3 The 3D visualization 3 1 4 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 Objects Atom H 3 Atom properties X 1 1064 y 1 015 A 2 A a Charge Molecules Y 1 butanol xyz a
15. the gradient view This can be viewed like a movie with the button OPen scan movie _ Page 56 64 6 Templates 6 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 use a template just choose a saved template from either Default Templates e or User Templates TmoleX will alter the settings accordingly generate start orbitals and brings you directly to the start job panel To save a template choose Save template from the Template menu of TmoleX Template Settings symmetry C Check O Molecular Charge Freezingpoint q 49999999E8 Level of theory RI Functional Grid Size SCF Energy 5CF Density Geometry Optimization Ground state Your choice Save As Template The settings are quite self explaining 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 e g 2 derivatives for post Hartree Fock methods are not supported by TmoleX excited states with TPSS are generally not possible COSMO calculations and frequency analysis is not supported either etc The template will have to be named when saving and can be found in the pull down menu afterward
16. windows 3 _0 exe To install TmoleX simply double click on TmoleX_ windows _3_0 exe and follow the installation instructions After installation TmoleX is available in your Windows Start Menu or as an icon on your desktop Please Note TURBOMOLE 6 2 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 e Numerical second derivatives script NumForce e 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 TURBOMOLE version for Windows 64bit includes serial and parallel 64 bit executables The parallel MPI version is only functional on Windows HPC systems with an installed version MS MPI Page 5 64 1 Installation 1 2 Linux Prerequisites Linux distribution based on Kernel 2 6 x The Linux version of TmoleX is distributed as a single file called TmoleX_linux_3_0 sh Please make sure that the file has execute permissions chmod a rx TmoleX linux_3 0 sh before starting it then follow the instructions on screen The full version of TURBOMOLE 6 2 is included in the TmoleX package Optimized binaries for a 32 bit Pentium compatibl
17. 0765545650 232 0765749310 232 0765749993 dE dxyz dE dxyz dE dxyz dE dxyz SCF energy SCF energy SCF energy SCF energy cycle cycle cycle cycle lt lt Previous Status Mos HOMO LUMO gap tatus Geometry Converged Converged Open Viewer 5 139 eV 3D Surfaces Gradients Open Files Vibrations y Output Energy 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 Ifthe 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 20 64 2 A quick tour 2 6 Job Administration File Edit Templates Help Tejas MEA A Prosas a a gt a a a Bs TmolexProject Job ID Job Director b Type Start Stop Machine 1 job GEO 1 GEO DFT RI B P charge 0 d6h def S Mar17 2010 3 local 4 job_ceo_1 job GEO choose Projectin Job Type gives a Start Stop for indicates a ProjectList to get very short timings and the geome
18. 3D visualization 3 4 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 selected will be by default the centre of the rotation Use the right mouse menu or the button gt or the key e to switch to rotation mode X TmoleX Project job 3 9 ae Page 36 64 3 The 3D visualization 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 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 Objects lt multiple selected gt F Rotate tool x C oH Protx 0463 y Hpo or z oF Photz _ am View OF 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
19. 790 418 4662744537 Gradients 210 2136469140 2414239803 418 4550708942 210 2135094552 1531746899 418 3666841450 Vibrations 210 2147523726 1812259629 418 3959783355 210 2156546666 2206481595 418 4363028261 Open Files 210 2163905640 2260125609 418 4424031249 210 2165387990 2234261331 418 4399649321 210 2165530170 2211536375 418 4377066545 210 2165689838 2215408280 418 4381098118 210 2165705518 2207893427 418 4373598945 210 2165711366 2211144425 418 4376855791 210 2165711681 2212578230 418 210 2165712088 2213451077 418 437916M165 210 2165712123 2213319921 418 tes CD Spectrum 210 2165712128 2212580631 418 4378292 q RAMAN Spectrum IR Spectrum NMR Shieldings Page 51 64 5 Constrained optimization and Scan jobs 5 Constrained optimization and Scan jobs 5 1 Defining fixed internal coordinates TmoleX 3 introduces a new way 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 FA TmoleXProject job 10 Label Edit additional label Guess length sj Guess dihedral angle i a y Change torsion a Measure torsion 5can ffreeze length Scan freeze torsion Delete On the right the options for freezing a bond length are show
20. AS IS WITHOUT WARRANTY OF ANY KIND EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABLLITY FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT IN NO 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 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 58 64 7 Remote jobs 7 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 a
21. GmbH amp Co KG TmoleX A Graphical User Interface to the TURBOMOLE Quantum Chemistry Program Package User manual COSMOlogic GmbH amp Co KG Burscheider Str 515 D 51381 Leverkusen Germany Phone 49 2171 363 668 Fax 49 2171 731 689 E mail turbomole Wcosmologic de Web hitp www cosmologic de Version 3 0 June 2010 Page 2 64 Table of contents o e E OO A A aa tetatone eseece 5 A VN CIOUNS ia te acute ene 5 2e MAMAN CR A no A E ns co epee seeade ate oeseete east canneries 6 To MaC OS aa E a ee eee eee eee ee 7 A AGUC VOU estos ie ad Sats gis sigs Saws ee gad gc Ae eae ae ieen amma ee a eel 8 Z Ne Starting Me programi ss esheets a 8 2 27 A MUS WaAlIVe examples Pa Mi A Os 9 2 94 Tho t00 An PP 10 24 The SOMO Sui Ai 11 20 NW Ss A EE A eee eat a dea Meo taislel 12 2031 Geometry panel il en iuedcauweanaiuatoxiee 12 202 BASIS SEU Hane lasir aaa e a a idos A 13 299 Molecular startorbitals Paneles a E E 14 204 Level of theory Select method nin a r a a otdysatecenasieb us aii aes 17 25 9 Start Job Select kindof jop and Star A A A 19 ZO ROSS a o od ae ee ee ee 22 207 JODAS IANO Viscose dis a 23 D C MOO VISU AIIZAUOM id a A E 2s 25 Soles TASU napa oia laos 25 Sl Navigator aaa An di id 26 3 12 Pro o A eC to OS et 21 A A 28 Sd Building Sep Dy SUC ibi 29 lo Change Donde lianas taa odio 31 A o a O AAAA 32 eee Change pond o A AAO 34 JO gt RIN AAA A o o denna sianiwiaat
22. R amp vibrational frequencies UV Vis and CD vertical excitations Raman amp vibrational frequencies Potential Energy Scan PES Qg _ Optical rotations dynamic polarizability Transition State Search Y Static polarizability Molecular Dynamics AIMD Y Single Point Properties Wi In the Results panel you can open the shielding constants in a text viewer File Edit Templates Help mea aa e y A ProjectList Geometry Atomic Attributes _ Molecular Attributes _ Gy TmolexProject Job Results Job Comparison y job_GEO_1 aia am Type of Calculation Single Point Calculation Status Mos Converged y job_SP_7 P job HOMO LUMO gap 6 008 eV Energy Open Viewer TextViewer shielding 3 3DSurfaces Gradients nmr dft shielding constants Vibrations NO TYPE MULT ISOTROPIC ANISOTROPIC dD dB CONTRIBUTION 1 124 68417067 48 26424712 120 95325152 36482667 76 43304950 93 30356234 11384951 6 41049676 0 49184925 Output 07942646 8 40559751 1 65737636 43044953 10902584 1 18216998 Energy 33871461 82239904 108 53069333 07556487 53137260 0 73496888 66692917 43798854 0 86155992 54275046 59866779 85 19564342 91877876 94829273 2 35260205 18239454 61365759 2 81674418 o pa Open Files Moments UV Vis Spectrum CD Spectrum RoOowco Jansen ryrprrarsrsy yo PRPrPPRPRrPRrPRPRPP Rh op a 5 A
23. RI Basis set def SV P Symmetry c1 Convergence Parameter Energy 10 Use resources Memory Disk Number of CPUs 250 0 MB for RI and spectra o MBforHF Delete scratch files after run Save and Run wE Run network Choose IR amp vibrational frequencies in the Start Job panel and click on Run Page 46 64 4 Properties The IR spectrum can be found in the Results panel de Tmolex 3 0 TIP gt l File Edit Templates Help Daaah B y poetuTempiates v vserremiates arasusizaa A Proeaus Geometry Atomicambutes Molecular Attributes _Memod ___StartJob_ Results Bs TmolexXProject y job_GEO_1 J ob SP 7 Type of Calculation Single Point Calculation Status Mos Converged jo Job Results Job Comparison af oo_ceo_s HOMO LUMO gap may ev Status Geometry Not Performed Energy Open Viewer zero point VIBRATIONAL energy 0 0978164 Hartree 3D Surfaces SCF energy 232 0765750 SCF E vib0 231 9787586 Gradients Vibrations Vibrational Modes Vibrational Spectrum Output mode symmetry wave number IR intensity selection rules cm 1 km mol IR RAMAN Energy 0 00 0 00000 0 00 0 00000 Moments 0 00 0 00000 0 00 0 00000 UV Vis Spectrum 0 00 0 00000 0 00 0 00000 CD Spectrum 401 72 0 00002 47 0 00008 RAMAN Spectrum 600 69 0 00000 600 72 0 00000 ES IR Spectrum 670 21 87 98809 74 0 00000 NMR Shieldings
24. Vibrational Modes IG Internal coordinates DD Builder Orbital Viewer i TmoleXProject job 2 plot 2 Scalar field IO 12 ab 1a2u 0 3308 4 ma Display isosurface w Max lt 0 15635078 0 039 Min gt 0 0 There are a lot of options and possibilities when visualizing 3D surfaces The most important things are 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 The Display options are o Isosurface use one iso value to plot the surface at this value o 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 o Isoplot plot a plane or an arbitrary surface which can be given as implicit equation like x2 y22 z22 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 If you see nothing not enough or not enough colours change Min and or Max value o 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 This will result in a 2D surface which represents the iso value of the density Page 44 64 3 The 3D visualization and the col
25. a EJ Favorites Ei Save 7 gimp 2 6 Contacts ci Links C4 Sea Li jchempaint Li COSMOmic Ei Mein Backup Datei Ci test L tmolex LT COSMOmic Tests C Music A Tmo LI 2 chlorophenol anion 3 Desktop LI my programs LI Tmo LI aceticacid LI Documents EI Novartis LI Tmo 3 amide p benzene C Downloads EJ Pictures L3 Tmo A II222O CilsersihuniadTmolexXProject 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 Page 8 64 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 The button rey in the tool bar or the menu Import Coordinate File in the pull down menu File will open a file browser on alalalBE File Name 0 Files of Type all coordinate files Select the coordinate file and load the molecular structure of benzene in TmoleX first change to the installation directory COSMOlogic10 TmoleX prefabs aromatics Page 9 64 2 A quick tour 2 3 The tool bar AN File Edit TC Jer ProjectList oe ep sm Molecular Attributes By TmolexProject Coordinates amp Symmetry E job_notRun_1 o eT a PP The tools in the tool bar act only on the job that you are
26. ackground 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 e To display labels of one or several atoms bonds only use the right mouse menu Label H 1 Symbol i Edit additional label I Number I ys Select bond partners Additional Substitute with gt Change element b Coordinate Arrange Saturate Page 34 64 3 The 3D visualization Own text can be entered in the second item of the 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 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 Labels gt Edit additional labe Invert selection A A _ a Translate E Rotate Scale b Create bond Create group o select two bonds measure angle e RP i pn Labels b Edit additional labe Invert selection Translate gt A Rotate a Scale Change bond angle Measure bond angle Scanifreeze bond angle Swap bonds Delete o select three bonds measure torsion Objects lt nothing selected gt w i hi l d Measures can be selected and deleted with the Measures pull down list nothing selected w Delete Bond properties Page 35 64 3 The
27. ataotaets 35 za ECO DUMIZ AO M oaro a a Gace dd ve cteuuanaebenmseaascele aa 36 3 3 Labels ana Measurement sumtadoss dial taa Seaboradeaetene 37 94 MOVING Rotating Scal usais a a 39 2 THE Jaden VIC We ena ocios 42 20 SU aC E POS lo 44 AP PP o E E E T EE 49 Ai Vibrational FegdUeNC ESen a a p a a i a 49 Az MRS PEC sl 52 4 3 Nuclear magnetic Shielding oocccooncoocnccconcconncconnonannonancononcononcnnnnnonnnnnnnnnnnnnnnonnnnnnncnnnncnnnnnnanennnnns 53 4A UVNisand CD Spectra TD DF P cuanal A a a reueceieeeees 54 5 Constrained optimization and Scan JODS ccccccccccsssccceeeeccensecceueeccuseccseucecsueeecsueeecsueesseueesssueessgeesseseeseeenass 55 5 1 Defining fixed internal COOFrdiNates ccoonccccoconoccnnccconononoconononononncnnnnnnnnnnnnnonnnnnnnnnnnonannrennnnenannennenanenos 55 32 Se Inte Mal Coordinate Sessu a aiii a a a dei 57 9 9 Sacos raned Optimiza dON sssrinin illa Modookadddueddanbnindebssadtuledcstelbidaeiadth 57 5 4 Scan along an termal COMAS ii 58 O O A A eee 60 Page 3 64 7 Remote jobs dll E E oa 61 7 sls SCC to Malo rias 61 22 AGA NEW remote Mac Mr ai 62 fos SAATE mole JODA A EE 64 CAs USM A qUetiInges St Midi A A A E 65 Page 4 64 1 Installation 1 Installation 1 1 Windows Prerequisites Windows XP Windows Vista Windows 7 or Windows HPC2008 The Windows version of TmoleX is distributed as a single executable file called TmoleX_
28. aturate Arrange Arrange hydrocarbons z Atoms misc Saturate anthracene 11 butanol xyz lt gt Delete rings Azulene 7 5 Ring jethanol xyz small_common c60 lisopropanol xyz methanol xyz ltert b utanol xyz ferrocenyl OH Indole ey matics naphthalene benzene xyz NH2 ponyls Norbornane Quinuclidine e as Molecule Delete Molecule x 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 saving molecules to this data base it is possible to select an atom when saving This selected atom of the stored fragment is the connecting atom Page 32 64 3 The 3D visualization 3 2 Preoptimization 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 Add atom Add molecule e Center molecule Clean up molecule Saturate all Guess bonds A simple rearrangement which minimizes the overlap of the van der Waals radii of all atoms b b e UFF a universal force field as implemented in TurRBomoLe can be used by clicking on the FF button le EF i e The recommended way is to use MOPAC 7 which is included in the default installation of TmoleX p E
29. ble 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 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 select Settings Note runs only on Linux Unix systems ServerilP Number of CPUs h User Saal Queue 5 No Password fo O Yes Add new clear Check password Settings Please select the working directory and the TURBOMOLE binary directory Work Directory TURBOMOLE directory Check every E min Cancel Save Settings General informations about a remote system are 1 The name or the IP address of a remote machine Server IP field 2 User name on that machine 3 Password to log in Those three field 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 Page 59 64 7 Remote jobs 4 Work directory tells TmoleX in which path on the remote machine the job shall run a local fast disk should be chosen here 5 TURBOMOLE directory has to be set to the TURBOMOLE installation directory on the target system Th
30. currently working on i e which is opened in the project list Create new job within the current project Read or import coordinates besides TURBOMOLE also xyz car sdf ml2 arc cosmo chem3d format Open existing control file either from an existing job directory or from external sources Save current job to disk file browser is being opened EJ Save Export current coordinates in various formats E 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 Edit control file this is the central input file for TURBOMOLE jobs This feature can be used to change or add keywords i e also to add features that are not directly supported by TmolexX Job templates Choosing a template from the default ones that come with TmoleX or from the ones the user has saved before will automatically set up a job with User Templates saved default settings See chapter 6 for details about templates Page 10 64 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 On the left you will find a list of open projects and jobs of each project 2 onthe top the general task menu Geometry Atomic Attributes Molecular Attributes etc 3 in the main frame the data assigned to the chosen task The i
31. dinates amp Symmetry aff oo_ceo_1 ra Import Coordinates File ee Open 3D molecular Builder E job_notRun_2 Atomic Symmetry Number of atoms 0 Current point group C1 Max tolerance 0 001 au Autodetect symmetry New atom N int ew point group Ct A new point grou Delete selected atoms pply ae 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 File View Tools Window Help MX 9 Alla ra F TmoleXProject job 2 Objects lt nothing selected gt 1 e e i d 9 F BBD Molecules Atoms Molecule J alcohols mm 3 1 butanol xyz gt d e B ethanol xyz a b isopropanol x z E methanol x E tert butanol Wz GJ aromatics benzene xyz E3 carbonyls E carboxylicacid xyz IN formaldehyd xyz y Save as Molecule Page 23 64 3 The 3D visualization 3 1 1 Left mouse button or or q on the keyboard Right mouse button or Middle mouse button or Eg Scroll wheel or Tay JTmolex visualizatio Select Rotate view Move Zoom File View Tools Window a E Al a te W TmoleXProject job 2 LMB Click or drag to select RMB rotate MMB move wheel zoom Page 24 64 Navigation Objects lt nothing selected gt Molecules Atoms C5 Molecule J alcohols Cy 1 butan
32. e CPUs and 64 bit platforms AMD64 and EM64T are available and will be chosen automatically by the script sysname 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 6 64 1 Installation 1 3 Mac OS Prerequisites Mac OS X 10 5 The Mac OS version of TmoleX is distributed as a single file called TmoleX_macos_3_0 dmg To install Tmolex simply double click on TmoleX_macos_3_0 and follow the installation instructions After installation TmoleX is available in the chosen folder by default in Application COSMOlogic T moleX3 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 S TURBODIR to the TURBOMOLE directory of the TmoleX installation and extend the PATH to STURBODIR scripts and STURBODIR bin sysname the binary directory Page 7 64 2 A quick tour 2 A quick tour 2 1 Starting the program Starting TmoleX for the first time you will be asked to choose a directory for your first project a Create Choose New Project Directory ok llame J cosmothermx Ei AppDat
33. e default behaviour of ssh when starting remote jobs without an 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 if the job is still running or not The frequency for those checks can be given in minutes 8 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 save settings and the machine with user name and paths will be suggested as name which will be added to the pull down list of machines for future usage Page 60 64 7 Remote jobs 7 3 Start a remote job Starting jobs can be done by choosing a machine in the list of saved systems Note runs only on Linux Unix systems Load Settings Delete Settings 1 Queue 5 No essees Yes Add new clear Check password Settings Please select the working d
34. f SV P Symmetry C1 Convergence Parameter Potential Energy Scan PES Potential energy scan Energy 49 Density Transition State Search Q Caution constraint geometry Molecular Dynamics AImD You have fixed internal coordinates Potential Energy Scan PES Options List of all fixed constraints Constraints Stepsize stre N9 H5 Use resources Memory l MB for RI Create new constraints by selecting bond s Disk MB for HF Unrelaxed scan no geometry optimization Relaxed scan geometry optimization at each point Number of CPUs Use current structure for all Generate each start structure from previous step v Delete scratch files after run This will cause TmoleX to generate just the first structure then take the optimized coordinates for the next steps later on Options Convergence criteria Energy 10 Hartree Gradient norm dE dxyz 10 Hartree Bohr Max no of cycles Run local Save and Run Save Use internal redundant coordinates Run network lt lt Previous 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 Dutton 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 Unre
35. freeze bond angle A benzene xyz Swap bonds Ed carbonyls o gt carboxylicacid xyz Delete HT tormaldeydaye el Translate Rotate 1 gt alcohols Save as Molecule Delete Molecule 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 XProject job 2 or E UDJECIS lt murupie serectea gt v Change bond angle Angle 106 652 small fragment big fragment Molecules Atoms Molecule EJ alcohols E 1 butanol xyz E 4 ethanol xyz 4 isopropanol xyz 4 methanol xyz 4 tert butanol xyz GJ aromatics Pie ol es Page 31 64 3 The 3D visualization 3 1 8 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 File View Tools Window Help Mx 9 Al y er A TmoleXProject job 2 Objects Atom H 8 Atom properties Element H A Label x gt Y Edit additional label y 4 Translate 1 Select bond partners Charge Substitute with alcohols Hybridisation custom A a te o Change element aromatics Coordinate carbonyls S
36. hat when being asked for If you use constraints or scan jobs internal redundant 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 where such jobs are started TmoleX 30 lt A Xx File Edit Templates Help Py 3 ray a ey p y Default Templates M User Templates M f Projectist _Seomety Atomic Attributes Molecular Attributes memos Resuits 7 Bs TmoleXProject Start Calculation af o0_ceo_1 Job type e af job_sP_7 af jov_ce0_2 Geometry Optimization Y Ground state Level DFT Functional b p y job_SP_9 Spectra amp Excited states Q gt oa v Ri wf job_sP_t0 Single Point E job_notRun_11 Single Point Properties Q Basis set def SV P Symmetry C1 Potential Energy Scan PES Conv eas nergy 10 Density Transition State Search Q Caution constraint geometry Molecular Dynamics AIMD You have fixed internal coordinates Options Convergence cr
37. iles kinetic energy 229 29024220481 Output potential energy 461 36681723033 Energy Gradients Moments cycle SCF energy 232 0757924401 dE dxyz 018808 cycle SCF energy 232 0765545650 dE dxyz 003179 UV Vis Spectrum cycle SCF energy 232 0765749310 dE dxyz 000174 cycle SCF energy 232 0765749993 dE dxyz 000182 CD Spectrum RAMAN Spectrum IR Spectrum NMR Shieldings The progress and status of all calculation belonging to your project which are currently running or ran 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 Page 22 64 3 The 3D visualization 3 The 3D visualization 3 1 The builder To open the molecular builder click on either the button in the tool bar or the button in the Geometry panel of Tmolex File Edit Templates Help Po Fa ta ey p Yy Default Templates User Templates Bs TmolexProject Coor
38. ion 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 i e DFT with empirical dispersion correction with or without RI J e MP2 e CC2 e SCS MP2 spin scaled MP2 e SOS MP2 scaled opposite spin MP2 e CCSD e CCSD T Page 16 64 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 Level of Theory SCF Convergence Solvation SCF convergence parameters Energy convergence 10 l IH artree Density convergence Example 1 0d 8 Max number of SCF iterations 30 Advanced settings DIS damping Start 0 700 Min last 0 100 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 TURBOMOLE 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 g
39. irectory and the TURBOMOLE binary directory Work Directory iometmolewTurbomole Jobs TURBOMOLE directory JRBOMOLE_62 TURBOMOLE A simple click on Ok 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 o x File Edit Templates Help aa JLE O y perau tempures gt Ee projects Bs TmoleXProject y job_GEO_1 aff iob_sP_7 yp p Machine SS E x GEO DFT RI B P charge 0 c1 def SV P O May 28 2010 11 32 0 May 28 2010 11 32 2 y job_GEO_8 job_SP_ SP DFT RI B P charge 0 c1 def SV P FR Jun 1 2010 10 49 24 Jun 1 2010 10 51 55 af joo SP 9 job_ a GEO DFT RI B P charge 0 c1 def SV P O Jun 1 2010 10 58 28 Jun 1 2010 10 59 23 OS job_SP_ SP DFT RI B P charge 0 c1 def SV P NMR Jun 2 2010 12 00 07 Jun 2 2010 12 00 12 y job_SP_10 job_ SP DFT RI B P charge 0 c1 def SV P EX Jun 2 2010 12 03 23 Jun 2 2010 12 03 31 af jov_sP_14 j gt SP DFT RI B P charge 0 c1 def SV P Jun 2 2010 11 20 32 Run 10 0 0 250 4 job_sP_15 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 61 64 7 Remote jobs 7 4 Using a queuing system Currently PBS and LSF are succe
40. ise back and forth Page 40 64 3 The 3D visualization 3 6 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 3D surface Y F r 4 j E MO File Edit y Ry FrojectList gt i i r Ba TmolexProject y job_GEO_1 y job_SP_2 Templates Help Geometry Type of Calculation Energy total energy kinetic energy Potential energy lt lt previous Job Results Job Comparison Single Point Calculation Molecular Attributes Status Mas HOM LUMO gap Status Geometry 1 70 936564059622 169 45604263959 340 39950355561 Page 41 64 Method Converged 3D surfaces Gradients vibrations output energy moments spectrum cospectrum shielding p i Open Files 3 The 3D visualization In a following window you will be asked which property to calculate By default the quality is set to quick Please note that the calculation in normal resolution might take quite some time What do you want to visualize Molecular orbitals _ Density total spin MP2 excited state derivates response _ Electrostatic properties potential field field gradient Quality Reduced resolution quick O Normal resolution slow For most users the molecular orbital will be
41. iteria Memory 250 0 MB for RI Energy 6 10 Hartree Disk lo MB for HF Gradient norm 3 ant dE dxyz 10 Hartree Bohr Pane ee EE Max no of cycles 50 lv Delete scratch files after run Use internal redundant coordinates Save and Run If you have frozen bonds angles or torsions make sure to use internal redundant coordinates otherwise your settings will be ignored 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 54 64 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 defined as fixed Help HANEL FR ProjectList 7 Bs TmoleXProject y job_GEO_1 y job_SP_7 y job_GEO_8 Geometry Optimization Level DFT pa Functional b p y job_SP_9 Spectra 8 Excited states Y aff iod_sP_10 Single Point Y job_notRun_11 Single Point Properties Y R Basis set de
42. iven 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 increased See the TURBOMOLE manual for details about DIIS Page 17 64 2 A quick tour 2 0 0 Start Job Select kind of job and start it In the Starto panel a single point energy calculation can be started File Edit slaaf Help ProjectList y Bs TmolexProject Results job_notRun_1 Job type Method Geometry Optimization O Level DFT Functional b p Spectra amp Excite RI Single Poin Basis set def SV P Symmetry ci Potential Energy Scan PES O Convergence Parameter Energy 10 Density Transition State Search Y Molecular Dynamics AIMD Use resources Memory 250 0 MB for RI Disk lo MB for HF Number of CPUs Delete scratch files after run Save and Run i Run D oo 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 Run network starts the calculation on a remote Linux Unix computer see chapter 7 Page 18 64 2 A quick tour Click through the Job type options to see what kind of jobs are sup
43. laxed scans and relaxed scans are possible single point or geometry optimization calculations will be done Page 55 64 5 2 Use internal coordinates 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 The job can then be started as usual also as a remote calculation A typical result is shown here File Edit Templates Help nakaw Default Templates v User Templates v 92 0172 2 MB Atomic Attributes Molecular Attributes Method Start Job Results 9 Bs TmoleXProject Job Results Job Comparison job_GEO_1 y job 97 Unit Open scan movie El e Ml j Scan directo Zero Value Ener Job_GEO_8 n 1f1 0t0rs9831 a job_SP_9 10 120 0281E 3 A Po 20 4447396E3 20 882 5256E 3 job_SP_14 40 1 312689 0 m 50 1 62599E0 60 1 749472E0 o El job_ceo_16 70 1 660876E0 o l job_ceo_19 80 13852160 90 990 2719E 3 gt jov_ceo_21 574 657E 3 l job_ceo_23 110 2487076E 3 98 50191E 3 y scan_0 Y scant y scan_2 y scan_3 y scan_4 y scan_5 y scan_6 y scan_7 y scan_8 y scan_9 y scan_10 Y scant y scan_12 The final optimized structures are stored for each of the scan points in a multi coord file similar to
44. nd 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 19 64 2 A quick tour 2 5 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 Help als al a a B Y omuntemoos gt isertonsoos gt Marana A ProjectList as TmoleXProject wf o9_cE0_1 _Seomety_ Atomic Attributes _ Molecularattibutes Job Results Job Comparison Type of Calculation Geometry Optimization Geometry Convergence Criteria convinfo energy change geom gradient 0 1000E 05 0 1000E 02 0 6830E 07 threshold 0 6740E 04 threshold actual value actual value Eneray total energy 232 07657502552 229 29024220481 461 36681723033 kinetic energy potential energy Gradients 232 0757924401
45. nput is divided into four different sections The kind of job or property that shall be calculated can be set in the Start Job panel s Start Job Results after a successful run can be viewed and further investigated in the Results panel You should follow the menu structure in the main frame from left to right The traffic light colours 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 Page 11 64 2 A quick tour 2 5 An illustrative example Part 2 2 5 1 Geometry panel section Here you can choose the symmetry File Edit Templates Help naaa FP ProjectList Start Job Results Bs TmolexProject Coordinates amp Symmetry A job_notRun_1 o E Import Coordinates File p Open 3D molecular Builder Units la v Atomic Symmetry Internal coordinates Number of atoms 12 A Current point group c1 Set of redundant Max tolerance 0 001 au Autodetect symmetry internal coordinates New atom New point group c1 Apply new point grou View internal coordinates Delete selected atoms poin group Number Element Fixed cartesian Fixed internal
46. of most interest Select occupied or unoccupied orbitals and proceed with next to the calculation Hold lt Shift gt or lt Control gt key to mark a list of orbitals y n ze Choose Molecular Orbital s to Calculate Nr spin symmetry energy degen YN NH N N NM N O DD O OOOD Page 42 64 3 The 3D visualization Click on Next to proceed A progress bar is shown Progress orbitals 11 Stop Calculation 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 etc 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 property 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 Open the Viewer with the Following Property Choose orbital No Spin Symmetry Energy H Degeneracy 19 ab 1 a 0 065 i 18 ab la 0 0233 17 ab 17a 0 1975 16 ab l a 0 2208 7 Choose property to view Open in Last Window Open in New Window Cancel Back Generate New Property Page 43 64 3 The 3D visualization a E Gradients
47. ol xyz ethanol xyz isopropanol xyz NE methanol xyz ES tert butanol xyz J aromatics IN benzene xyz Gq carbonyls carboxylicacid xyz A formaidenydxyz Save as Molecule A 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 TmoleXProject job 2 rn r Molecules Atoms E Molecule J alcohols D 1 butanol xyz a ethanol xyz isopropanol xyz D methanol xyz a tert butanol xyz matics D benzene xyz J carbonyls a carboxylicacid xyz IN formaldehyd xyz lv Save as Molecule The molecules in the right part of the window are by default taken from the prefabs directory of the TmoleX installation This can be changed to a user defined directory in the Tools Visual settings menu The files are stored in standard xyz format the second line can contain the name of a fragment with the General Atoms Bonds Labels Properties Path Grid Misc Fragments Database iprefabs Browse Scan depth i 2H definition of the number of atom which can be replaced see the files in the TmoleX prefabs directories The Save as Molecule button can be used to store the
48. olexProject Job Results Job Comparison of 1o0 cE01 Type of Calculation Geometry Optimization Status Mos Converged HOMO LUMO gap 5 139 eV Status Geometry Convergec Geometry Convergence Criteria Open Viewer convinfo O g 3D Surfaces energy change actual value 0 6830E 07 threshold 0 1000E 05 geom gradient actual value 0 6741E 04 threshold 0 1000E 02 Gradients Vibrations Energy total energy 232 07657502553 A Open Files ee a Output kinetic energy 229 29024232226 potential energy 461 36681734779 Energy v aan cycle a SCF energy 232 0757924315 dE dxyz 0 018808 UV Vis Spectrum cycle 2 SCF energy 232 0765545647 IdE dxyz 0 003179 cycle 3 SCF energy 232 0765749310 IdE dxyz 0 000174 CD Spectrum cycle 4 SCF energy 232 0765749993 IdE dxyz 0 000182 RAMAN Spectrum IR Spectrum NMR Shieldings lt lt Previous Page 39 64 3 The 3D visualization The total energies for the optimization steps can by viewed here Ie Internal Coords ee Builder E Orbital viewer HN Objects de cosmologic cosmobuild c Gradient Energy 210 21657 210 205521 LME Click or drag to select RME rotate MME move wheel zoom The different geometry can also be viewed as a movie by using the play buttons or moving the slider The smaller lt and gt go stepw
49. 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 charge freeze core orbitals for correlated calculations or switch on Fermi smearing Switch from Table to Diagram to see the usual orbital occupation graphics Use the left mouse 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 15 64 2 A quick tour 2 0 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 2 TmoleX 3 0 1 File Edit Templates Help 10000 ay eraun Tomoates gt fusertemiases assraamal f ProjectList Molecular Attribut Method Bs TmoleXProject Level of Theory SCF Convergence Solvation job_notRun_1 Lal DFT y Use RI Element Basis set Auxiliary basis set DFT settings ESA id H def SV P def SV P v Functional bes Gridsize 4 43 Auxiliay basis sets for RI J Activate COSMO Filename lt lt Previous Continue gt gt The level of theory for your calculat
50. our 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 o Isosurface plots two iso densities one at the positive value and one at the negative value A typical molecular orbital picture 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 Page 45 64 3 The 3D visualization 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 Help PY ProjectList Bs TmolexProject Job type Geometry Optimization Y Single Point Properties Wa Potential Energy Scan PES a Transition State Search 4 Molecular Dynamics AIMD Frequency analysis 2 All frequencies O lowes eigenvalues No of frequencies C Numerically Cumently not supported by Tmolex IR amp vibrational frequencies UViVis and CD vertical excitations NMR shieldings Raman amp vibrational frequencies Optical rotations dynamic polarizability Static polarizability Level Functional b p
51. ported by TmoleX File Edit Templates Help aala a lE ey ay seremos sereme 29212008 a Projects Atomic Attributes Molecularattributes Method startWob Bs TmolexProject Start Calcuintion job_notRun_1 Job type Method Geometry Optimization O Ground state Level DFT Functional b p Spectra 8 Excited States IR amp vibrational frequencies A RI Single Point UV Vis and CD vertical excitations ee NMR shieldings Basis set aive Symmetry c1 Raman amp vibrational frequencies Convergence Potential Energy Scan PES A i 5 Optical rotations dynamic polarizability Energy Density Transition State Search Static polarizability Molecular Dynamics AIMD Q Use resources o Memory MB for RI Options ae MB for HF Convergen Energy 40U Hartree Number of CPUs Gradient norm dE dxyzj 10 IHartree Bohr lv Delete scratch i after run Single Point Properties Max no of cycles Save and Run Use internal redundant coordinates L Rungoca Save Run network lt lt Previous 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 space for the calculation If a
52. s Page 57 64 7 Remote jobs 7 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 7 1 Security information To determine if you do want to use this feature and worry about security here is a short 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
53. ssfully tested Activate the queue option in the remote job start panel select Settings Note runs only on Linux Unix systems tmolex 10 0 0 250 Load Settings Delete Settings Server IP 10 0 0 250 Number of CPUS A User tmolex Queue D No Password essees Yes Add newiclear Check password Settings Script to start Job enter here Please select the working directory and the TURBOMOLE binary directory Work Directory lometmolerTurbomole Jobs TURBOMOLE directory JRBOMOLE_62 TURBOMOLE Submit with qsub Check every E min Check status lastat cancel Save Settings Ok 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 ASUS is the default For LSF it should be bsub lt 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 Page 62 64 7 Remote jobs Tmolex 3 0 TIP io Bas File Edit Templates Help A ProjectList j TmoleXProject af 00_cEo_1 af ob_sP_7 af oo_ceo_s af 00_sP_9 eff ob_sP_10 af job_sP_14 wf 00_sP_15 El iob_ceo_16 scan_0 scan_1 scan_2 scan_7
54. try a list of all jobs description of the status if job is still optimization most important running settings 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 not remote jobs without a queuing system for remote jobs which run under a queuing system the status of the queue is shown A ProjectList Bs TmolexProject aff iob_cEO_1 3 job_sP_7 P NE de ES WPIFR J r jose Show this Job Close this Job Stop this job View Job directory Delete this Job Page 21 64 2 A quick tour File Edit Templates Help Beda Bs TmolexProject y job_GEO_1 Type of Calculation Geometry Optimization Status Mos Converged HOMO LUMO gap 5 139 ev Status Geometry Converged Geometry Convergence Criteria Open Viewer convinfo 3D Surfaces energy change actual value 0 6830E 07 threshold 0 1000E 05 geom gradient actual value 0 6740E 04 threshold 0 1000E 02 Gradients Vibrations Energy total energy 232 07657502552 a Open F
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