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TmoleX - COSMOlogic

1. C Freeze Length Scan Length LJ Freeze Torsion Scan Torsion Guess Length 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 q a gt Bond Atom Style b Label P Edit additional label Measure torsion Scan freeze length Scan freeze torsion cree anoano Page 36 85 3 The 3D visualization 3 4 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 El e a Bond Atom Style Label Edit additional label Measure torsion Scan freeze length Scan freeze torsion Guess length Guess dihedral angle Change torsion h 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 Tmol
2. 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 Wcosmologic de Web hitp www cosmologic de Version 4 0 May 2014 Page 2 85 Table of contents A otek see fete oases See cere nae te heen ee uae oecare ec aee Gem geste eee acc enmaee co eacreaee yaeee eae en aotemeemcacena ee een seen 5 A sees Aged Saga abacw mses emcees eee ea a 5 A Ann e En Games tmenea 6 FMIC OSa ete em eee ee er ete ee 7 T4 Oline UBdateS A Ay ovat daw tense A aecse cee as 7 SA O eats ed ee eed alee aa Aas beat guage anal care eee 9 2 Starting TAS PoJ Maita ai AN tt 9 ZLA AN MUsStative example Rara ita 11 a TRE OOl AAA Po ctatend ney te dpai sad opted a A toenail bla tet as oe slat tat sale laa 12 e a a letra ate cit me lama eet Stands ieee de Cathe alts oles acne Dhaba ld 13 ZD AM MUS atve example PAN 2c id o ali de 14 ZO A AGEOMEWY Dalt A ii i 14 2 0 2 BASIS SELANE iron a dct oven ose deiad iad a a a asda tae hee ean ors eee ae dee 15 2 9 5 Molecular startorbitals Dan Cl ssectuses seeds eee Ge tne kao nas 16 2 54 Level of theory Select method eiiieaen a o ded 18 2 5 5 Start Job Select kind of job and Start it ooocccooonnccccnncconncnoncnnocanonoconononannnnnannnonnnnnnnnnncnnnnnenonanos 20 2 O
3. Click Ok The generation takes only a very short time to compute and the initial molecular orbital are displayed oa x A ee E A O ea er E e v E ProjectList l Y 5 TmoleXProject Bl job_notRun_1 Choose Job Template Charge v Apply Job Template Molecular Orbitals OO Molecular Orbitals Table Diagram Molecular charge 0 wt DD eee ee a ae Multiplicity Singlet y roy ocupe OS ry ccned_ nD Generate MOs Delete MOs Advanced settings Fermi settings Fermi Frozen orbitals for MP2 CC2 _ Freezing point Hartree 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 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 17 85 2 A quick tour 2 5 4 Level o
4. Labels E Edit additional label y ren soecion E Translate gt l Rotate Scale gt e b Merge overlapping atoms Add atom at center Create group iii 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 32 85 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 gt Bond Atom Style Ss gt s a Invert selection gt 7 7 Scale Ring conformation gt Add atom at cLater Create group Copy Cut Delete The trick to set a bond length to zero works only in cases where the selected bond is not part of a ring Page 33 85 3 The 3D visualization 3 4 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 0 5254 0 898 A Charge i Hybridisation custom z Saturate Arrange Delete Molecules Atoms Y J Molecule Y J alcohols J 1 butanol sdf 1 2 propenol sdf ri othr Af On the right side the properties of the selected item
5. E 100 10 8 4 33 74 ridft mpi 5170 tmolex 20 Jj 583m 462m 3660 R 100 7 7 2 08 92 aoforce tmolex 20 2634m 1 23 1 13 E 38 20 6 5 01 87 ridft mpi root z0 1064 384 3274 5 GC 0 0 0 00 82 init root 15 a 0 a 0 0 0 00 00 kthreadd In the first line the load i e the number of running time consuming 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 76 85 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 vE ProjectList i Geometry _ y z _ z gt Y 5 TmolexProject e Y job_GEO_1 Choose Job Templat
6. GEO FREQ Save and Run Run local Save Run network Page 72 85 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 files 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 submit everything to a remote system button to use the system TmoleX is running on or the Run network button to While the job is running the icons in the job list on the left side of your TmoleX window will show their current status E 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 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 j 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 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 Fi job_BATCH_17 OPT FREQ xml Jun 4 2014 11 39 1 Running 10 0 0 250 On remote systems the resultin
7. RO NS A O Ree ae rt ee an am eng en ee Eee Se ee ere eee ene ee eee 22 ZO JOD AdMINSTAUO Nadia 23 LIME MISUAIZ MOM iodo eee 25 A a a a a a cum tnnaeoassbaree 25 3s lol INAVIG AION 5 a A E A 26 SAA llo e STUC AAA Po a a a aaa 21 SL IMPOR STC a o e esas 28 39 Easy DUNGING ato alto 29 3 4 Build complex molecules by Merging fTAQMEenNTS ccccooccccccconccccnccnncncnnncnonnnnnonncnononnnonnrnnonnrnnonnrnnnnncnnannnrs 30 24A DUNGIMNG Sie OV SIED dt o ic Doa 34 S72 Ghange Dond lentas i 36 24S Change A e y N 37 3 9 Change DOM ante rt tios 38 3 0 1 BUNGING step DY SIED Zoret e a a a a a a 39 A a ina 41 3 7 Labels and MEASUrEMENMS ccceccsecccececeeecseecececeueceeeceeecseessueesanesaeeceesaeecaeecaeesaeesueeseeesageeaueesueeseeesaes 42 3 0 MOVING Rotating Scala ide 45 39 he gradien VICW CM cis o dicidiads 48 IAS A tial osesent 50 A A aa 55 Al VIDEatlonal Tequentdies sica iS a a A diae dt Gcdahidodalan Ses 55 E A A Ma Mandalateiia E a 57 4 3 Nuclear Magneto Sms iIN csiita alado ii A id IS A ci laca 58 440i Vis and EOD spectra IDO Tui cortesia li tail iia cta 59 5 Constrained optimization and Scan joODS ccoooncccocnnccconnnconnnoconnnononnnonnnnnnnnnnnnnnrnnonnnnnnnnnrnnnnnnonannnnrannrennnnenannnns 60 5 1 Defining fixed internal COOFrdiNates cccoonccccconcccocnnoconnconononononnnonnnnnonannnnnnnnnonnnnnnnnnnnnannnennnnnenannennenannnns 60 90 2 Use Mena coordinate S aaz adds 62 92 art
8. arbitrary surface which can be given as implicit equation like x42 y42 Z42 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 and the colour on the surface is given by the value of the chosen property at that points Typical Page 53 85 3 The 3D visualization 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 Objects lt nothing selected gt M indie Max lt 541 17365 og Eo Min gt 3 4574777E 4 0 37 en Continuity hooo H Page 54 85 3 The 3D visualization 4 Properties 4 1 Vibrational frequencies If you have an optimize
9. from fragments and modifying these Double click on a fragment to import it in the builder J TmoleX visualization oS e es File View Edit Tools Display Type Window Help 6 a a gt O A cracients vi Modes Fie Internal Coords 3 Buider Orbital Viewer U TmoleXProject job_notRun_2 Number of atoms 12 Number of bonds 12 A Objects lt nothing selected gt Quickstart guide S ek Bos y rings IB benzene sdf J benzimidazole sdf J4 borazine sdf J imidazole sdf J indole sdf J1 pyrazole sdf a left mouse button Click or drag to select right mouse button rotate MMB move wheel zoom Page 25 85 3 The 3D visualization 3 1 1 Navigation Left mouse button or L3 or q on the keyboard Select Right mouse button or Rotate view Middle mouse button or a i Move Scroll wheel or al Zoom TmoleX visualization Fle View Edit Tools Display Type Window Help de in a CD G a a Gradients Vib Modes J Internal Coords go Builder Orbital Viewer Scan TmoleXProject job_notRun_2 x Number of atoms 12 Number of bonds 12 Objects nothing selected gt Quickstart guide Page 26 85 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 wind
10. network in the Start Job panel Save and Run Run local 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 Set Parameter for external Job Note runs only on Linux Unix systems Select settings vr Data for remote system Server IP max total number of CPUs User number of CPUs in use Password Check workload Check Password Settings Configure Work directory TURBOMOLE directory Number of CPUs for job s 1 Check every 1 j Check remote system Use queuing system Delete Settings Clear Add New Load Settings Cancel Save settings OK 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 Page 79 85 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
11. 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 e def TZVP Page 15 85 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 nat yet have valid start orbitals the button will remain red fs faa x File Edit Templates Results Extras Tools Help 3 Py ES a HE pS g Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex __96 5 151 5 MB System 0 0 6296 2 MB y E Projectlist Method Statlob SS Results Y 5 TmoleXProject ee oR A RE oo rennet menace ED RAAT ITT TR Choose Job Template v Charge y Apply Job Template Energy Hartree Degeneracy Occupancy HOMO LUMO Frozen orbitals for MP2 CC2 Freezing point Hartree Continue gt gt e Perform an extended Hueckel calculation Symmetry c1 i i Charge If you click on Generate MOs a message box will come up ee EHT AOS Bis H ox J cancel Do not forget to set the molecular total charge before generating orbitals for IONS Page 16 85 2 A quick tour
12. 0 120 lt lt Previous Manage Job s The final optimized structures are stored for each of the scan points in a multi coord file similar to the gradient Open Scan Movie view This can be viewed like a movie with the button 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 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 64 85 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 Read in existing template to mod
13. 5 Start Job Select kind of job and start it In the Starto panel a single point energy calculation can be started File Edit Templates Results Extras Tools Help 3 if gt a m 9p Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex _ 919 159 5 MB System 0 0 6296 2 MB v E ProjectList Y 5 TmoleXProject A 19 AAA AAA Choose Job Template Apply Job Template Start Calculation Job type Method Results Geometry Optimization gt Level DET Functional b p ARI Basis set def SV P Symmetry C1 Convergence Parameter Energy 10 Density Potential Energy Scan PES gt Transition State Search gt Templates gt Batch processing gt Use resources Memory used for 500 0 MB Disk 0 MB for HF No of CPUs 1 Delete scratch files after run Save and Run noc Save Run network lt lt Previous 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 8 Page 20 85 2 A quick tour Click through the Job type options to see what kind of jobs are supported by TmoleX 4 TmoleX 4 0 TmoleXProject E File Edit Templates Results Extras Tools Help a pa gH 5 89 open 3D Molecula
14. 72 0 00000 YES YES 1 a 670 28 87 98540 YES YES Save as job template for further us 12 a 712 74 0 00000 YES YES ES a 837 52 0 00000 YES YES ss anon nm nnn ma m v lt lt Previous IR 6 l ape a Select a specific mode and click play TmoleXProject job_SP_6 vibrations x Number of atoms 12 Number of bonds 12 600 69 0 00000 YES YES 600 72 0 00000 YES YES 670 28 87 98540 YES YES 712 74 0 00000 YES YES 837 52 0 00000 YES YES 837 81 0 00000 YES YES 955 56 0 00001 YES YES 955 89 0 00001 YES YES 983 83 0 00003 YES YES 993 07 0 00000 YES YES 998 23 0 00000 YES YES 1035 28 5 10903 YES YES 1035 46 5 17511 YES YES 1134 64 0 00013 YES YES 1156 51 0 00000 YES YES 1156 87 0 00000 YES YES goqvqegqgegdvgveqdqdqgoegdvedqgegqgegoqgegqgaegegagedqgeda gags ww Select one or several modes first Use the play buttons and or the slider to see the vibration Page 56 85 4 Properties 4 2 IR spectrum Use the 2 IR Spectrum to open the IR spectrum Graphics Table original data Unit 1 cm Std deviation 87 94 Min freq 117 7573 Max freq 3685 6661 Frequency shift 0 0 Sampling points 119 Broadened by Gaussian O Lorentzian EJ Line spectra Calculate min max NS ime Visual settings 1 000 1 500 2 000 2 500 3 000 3 500 1 cm Width line Line spectra Standard deviation for the broadening Gaussians or Lorentzains a frequency shift number of sampling points etc can be
15. CoNStTaNed ODUIMIZANON x5 vec os creat e a a N 62 5 4 Scan along aninternal coordinate tea in ii 63 Page 3 85 5 5 can along several internal coordinate S sienas dido 64 300 TOMPIAES aia tl crecen 65 0 1 Detine JON templates ii a EAS 65 02 ADDI JO EMI CS sie a a dbSdo 66 6 3 ResuliS OJD Templates sad Id 68 PACH processor dara la 69 7 1 Read IN ana Use several Molecules iio il ido a deeb Ulan ae 69 Generate batch jobs from existing jODS ccoocccccocncccononocononononoconnnnnonnnnnnnnnnononnnonannnonnnnnnnnnnnnonenenanenos 71 7 2 Apply templates for batch OD a ra aida 12 7 3 RUM Ocal OF TemoteDaton JOS la ba 73 7 4 Visualize and export results Of batch jODS ccoooccccoccnnccoccconocnnnnncnonnnnnonnnononnnnnonncnnnnnnnnonnrnnnnnrnnonannnnannnos 77 A A e io A 78 91 Se cun Ima EON tetera 78 9 2 NOG new Te mole Machine essa datada ippo 79 UE AMO OD tostada die A 81 8 4 Using a queuing system on a remote cluster cccooccoconccconccconcconncnonnnnanonnnnnnnnnonnnnnnnnnnnannonancnnannnnnnnns 82 s COMBINING Re SU Sissi solais 85 Page 4 85 1 Installation 1 Installation 1 1 Windows Prerequisites Windows XP Windows Vista Windows 7 or Windows 8 The Windows version of TmoleX is distributed as a single executable file called TmoleX_windows 4 0 exe To install TmoleX simply double click on TmoleX_ windows 4 0 exe and follow the installation instructions After instal
16. DFT RI B P charge 0 C1 def SV Jun 4 2014 10 43 Jun 4 2014 10 47 Local gt Py 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 Jun 4 2014 11 18 Local 17 job_BATCH_17 OPT FREQ xml Jun 4 2014 11 39 Jun 4 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 81 85 8 Remote jobs 8 4 Using a queuing system on a remote cluster Currently PBS LSF and SGE are successfully tested Activate the queue option in the remote job start panel Set Parameter for external Job Note runs only on Linux Unix systems Select settings tmolex 10 0 0 250 Data for remote system Server IP 10 0 0 250 max total number of CPUs User tmolex number of CPUs in use Password AEREA Check workload Check Password Settings Configure Work directory home tmolex Tmolex_Jobs TURBOMOLE directory softtware TURBOMOLE_66 TURBOMOLE Number of CPUs for job s 1 Check every 1 min Check remote system E Use queuing system Submit with qSsUb Check status stat Script before job execution without bin sh automaticaly add PARA_ARCH SMP MPI E add PARNODES number of CPUs Script after job execution Delete Settings Clear Add New Load S
17. PM Jun3 2014 9 55 27 PM A as SP DFT RI B P charge 0 c1 def SV P FREQ Jun 4 2014 9 59 40AM Jun 4 2014 10 01 58 AM Y scan 0003 SP DFT RI B P charge 0 c1 def SV P NMR Jun 4 2014 10 21 54AM Jun 4 2014 10 22 04 AM Y scan_0004 SP DFT RI B P charge 0 c1 def SV P EX Jun 4 2014 10 26 40AM Jun 4 2014 10 26 53 AM Y scan_0005 GEO DFT RI B P charge 0 c1 def SV P GE Jun 4 2014 10 38 31AM Jun 4 2014 10 40 46 AM Y scan_0006 GEO DFT RI B P charge 0 C1 def SV P G Jun 4 2014 10 43 11AM Jun 4 2014 10 47 00 AM v 7 job_SCAN_11 OPT FREQ xml Jun 4 2014 10 57 53 AM Running Y scan_0000 Y scan_0001 Y scan_0002 Y scan_0003 Y scan_0004 Y scan_0005 Y scan_0006 Y scan_0007 lll Y scan_0008 job no 0 is currently running H re iT o p Y scant pa Refresh Y scan_0010 o SCE SCFKIN SCFPOT Energy vs Geometry cycle a 1 194 2039480590 2805999062 386 4845479652 Y scan_0011 2 194 2047077801 1912148110 386 3959225912 194 2040 _ Y scan_0012 3 194 2047697520 1688533165 386 3736230686 v gt job_TEMPLATE_14 4 194 2047756935 1673543536 386 3721300471 194 2041 job_0000 5 194 2047781207 1686932171 386 3734713378 job_0001 194 2042 194 2043 SCF energy 194 2039480590 IdE dxyzl 0 028814 SCF energy 194 2047077801 dE dxyzl 0 008648 194 2044 SCF energy 194 2047697520 dE dxyz 0 002675 SCF energy 194 2047756935 dE dxyz 0 001452 194 2045 194 2046 194 2047 1 MUA qL _ _
18. P_8 o Add Molecule o Delete Molecule gt 3 job_SCAN_9 gt job_SCAN_11 gt job_TEMPLATE_14 a 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 te Add Molecule button This opens a file browser which also allows to read in file formats which contain multiple structures like sdf Multiple selections within the file browser are of course also possible Page 69 85 7 Batch processing Y job_GEO_5 Y job_SP_6 Y job_SP_7 Y job_SP_8 gt job_SCAN_9 gt job_SCAN_11 gt job_TEMPLATE_14 job_notRun_15 4 TmoleX 4 0 TmoleXProject Fle Edit Templates Results Extras Tools Help La fa pa a EH pS open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for TmokX 196 8 270 2MB Y E Projectiist Es Y 5 TmoleXProject Y job_GEO_1 EJES ad Choose Job Template System 0 0 6296 2 MB on Q Res m gt Molecular Attributes gt Atomic Attributes Y Charge a ultiple Coordinates e add Molecule methylamine ethylamine propylamine ia Janine Look In Test cases A 1 cosmo files A out_10 xyz CA out_11 xyz BigClus
19. Point Calculation Status mos Converged Open Viewer HOMO LUMO gap 5 139 eV Orbital Density Plot Status geometry Not performed gt radiant Energy ee A Senergy SCF SCFKIN SCFPOT 1 232 0757937330 229 4793919515 461 5551856845 2 232 0765545974 229 319562255 461 3961168523 3 232 0765749475 229 2916754907 461 3682504382 gt 4 232 0765750244 229 2903224021 461 3668974264 NMR Shieldings 5 232 0765750262 229 2902310651 461 3668060912 A TSE 6 232 0765750263 229 2902164707 461 3667914970 on end Open Files Output NMR Shieldings Energy nmr dft shielding constants M t 1 c 1 63 84369068 182 38424399 188 45435446 E 2c 1 63 84994381 182 39904285 188 57243313 Mi vss Spe 3c 1 63 84084530 182 38270866 188 45481295 oe 4c 1 63 84586533 182 38520047 188 45188219 BN co spectrun 5 c 1 63 85164377 182 40001089 188 57046808 les 6 c 1 63 8404269 182 38267219 188 45529017 lbs 7h 1 2455004417 5 53087549 5 08872411 Mn spectru 8 h 1 24 56448603 5 48342201 5 04958979 LS 9h 1 2455141466 5 53295887 5 08218234 ERTER 10 h 1 24 555027160 5 53118500 5 08910415 als 11 h 1 24 56467651 5 48368315 5 04989062 ca 12 h 1 2455138400 5 53289760 5 08211459 Watoa AA end Save as job template for further usagi lt lt Previous 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 m
20. RCHANTABLLITY 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 78 85 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
21. Templates Results Extras Tools Help 1 li a is H 5 89 Open 3D Molecular Builder Job Y E ProjectList Geometry Atomic Y 5 TmolexProject cnn cn gt gt choose x Stop this Job View Job Directory Open Shell ali ees job_GEO_1 Delete this Job View Run Status i j Page 23 85 2 A quick tour 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 Internal simple queuing system Set the number of cores of your machine in the Extras gt Settings menu Then TmoleX will take care of the number of jobs you are starting Jobs running local 1 4 remote O Memory used for Tmolex Saee anlel System 500 0 6296 2 MB 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 a
22. TmoleXProject eE PX File Edit Templates Results Extras Tools Help ae H a g Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 121 2 175 0 MB System 0 0 6296 2 MB y ca L_Seomet Start Job Results 5 roj f PPO Choose Job Template Charge w Apply Job Template job_GEO_5 Y hose Job Results Scan job result Job Comparison Results Multiple Jobs Comparison Movie Y job_SP_7 job_SP_8 Unit Hartree v Open Scan Movie O Em x ns pe HBa if p Eln f scan_0000 a Y scan_0001 Scan directory Zero aa 08 C3 Energy tad 4 scan_0002 scan_0000 DEO 154 9057E0 154 9059 al s y T scan_0001 9 154 9059E0 154 9060 r 4 scan 0005 scan_0002 20 154 9064E0 154 9061 Y scan_0006 scan_0003 30 154 9071E0 154 9062 By 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 9085 0 154 9065 Y scan_0002 scan_0007 70 154 9083E0 154 9066 8 Y scan_0003 scan_0008 80 154 9079E0 154 9067 4 scan_0004 scan_0009 90 154 9072E0 154 9068 Y scan_0005 scan_0010 100 154 9066 0 154 9069 Paipa scan_0011 110 154 9061 0 154 9070 i Y scan_0008 scan_0012 120 154 9058E0 154 9071 AL 154 9072 f Y scan_0010 pentane Y scan_0011 1542074 Y scan_0012 154 9075 154 9076 154 9077 j 154 9078 154 9079 P 154 9080 154 9081 154 9082 y 154 9083 N os 154 9084 10 20 30 40 50 60 70 80 90 100 11
23. Y 0 758 Z Pivot 7 0 67 View Around View Pivot at COM x 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 can also be entered manually if needed Note that the selected atoms which will be rotated do not have to be connected 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 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 46 85 3 The 3D visualization View Edit Tools Display Type Window Help daar e a a a Ds O Q a Gradients Vib Modes JO Internal Coords g Builder Orbital Viewer TmoleXProject job_notRun_4 x Number of ato
24. ___ o A EE 0 1 5 2 0 2 5 3 0 3 5 4 0 Here the first job a geometry optimization is running The status of this job is therefore printed as Energy vs the geometry cycle Page 67 85 6 Job Templates Multi template jobs will create sub directories for each individual job Selecting an individual job will present the 6 3 Results of job templates results of this step as for a usual non template job Selecting the template itself in the job tree will give a summary as table fa TmoleX 4 0 TmoleXProject File Edit Templates Results Extras Tools Help lya if z iS EH lamar g Open 3D Molecular Builder Jobs running local 0 4 remote Memory used for Tmolex 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 v 7 job_SCAN_9 Y scan_0000 Jf scan_0001 Z scan_0002 Y scan_0003 Jf scan_0004 Y scan_0005 Y scan_0006 v V job_SCAN_11 Jf scan_0000 Y scan_0001 Y scan_0002 Y scan_0003 Y scan_0004 4 scan_0005 Jf scan_0006 Jf scan_0007 Y scan_0008 Y scan_0009 Y scan_0010 f scan_0011 Y scan_0012 fy job_ TEMPLATE_14 Y job_0000 Y job_0001 Manage Job s 4 seome Atomic Attribute OPT FREQ xml SEE Charge Apply Job Template Job Results Scan job result Job Comparison Results Multiple Jobs Comparison Movie Project Name Job Name 2D structure Number of atoms Basis function
25. 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 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 Page 84 85 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 E ProjectList i Y 5 TmoleXProject Y job_GEO_1 Y job_GEO_5 Y Job Results Sc Y job_SP_7 Y job_SP_8 Type of Calculatior Y o job_SCAN_9 Z scan_0000 Y ESTA Y scan_0002 Z scan_0003 Y scan_0004 zero point VIBRAT Y scan_0005 SCF energy Y scan_0006 SCF E vib0 gt 3 job_SCAN_11 Y job_TEMPLATE_14 Y job_0000 job_0001 v job_BATCH_15 Y methylamine Wd ethylamine Vibrational Modes Y propylamine 22 Y aniline 23 v y job_BATCH_17 24 gt 3 TmolexProject_m 25 P ojah 26 gt y TmolexPre TmolexPrc Generate new Batch Job Y job_GEO_18 job_GEO_19 Energy Y Y Y y 0 TmoleX will gener
26. age 22 85 2 A quick tour 2 6 Job Administration TmoleX 4 0 TmoleXProject I a eS File Edit Templates Results Extras Tools Help aw law H 5 89 Open 3D Molecular Builder Jobs running local 1 4 remote 0 Memory used for Tmolex 98 5 152 0MB System 500 0 6296 2 MB y E ProjectList Atomic Attributes Molecular Attributes Start Job E TmoleXProject job_GEO_1 Choose Job Template Y MENE Job Template ESA K S 2014 4 10 5 TE rae job GEO choose Projectin Job Type gives R for indicates a ProjectList to get very short timings and the geometry a list of all jobs description of the status if job is stil optimization most important running 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 TmoleX 4 0 TmoleXProject File Edit
27. als down from the HOMO lines are given in blue and up from the LUMO lines are given in red 3D Visualizer Xx Choose Molecular Orbital s to Calculate No Spin Sym Energy Hartr Degen Occup HOMO LUMO IRE ab 55a 0 0834 1 0 LUMO 7 a 54 ab 54a 0 0519 1 0 LUMO 6 53 ab 53a 0 0421 1 0 LUMO 5 52 ab 52a 0 0255 1 0 LUMO 4 51 ab 51a 0 0099 1 0 LUMO 3 50 ab 50a 0 0213 1 0 LUMO 2 49 ab 49a 0 0607 1 0 LUMO 1 48 ab 48a 0 0869 al 0 LUMO 47 ab 47a 0 2229 il 2 HOMO 46 ab 46a 0 2253 1 2 HOMO 1 45 ab 45a 0 2378 o 2 HOMO 2 44 ab 44a 0 2445 2 HOMO 3 43 ab 43a 0 2749 1 2 HOMO 4 42 ab 42a 0 3045 1 2 HOMO 5 41 ab 4la 0 3147 1 2 HOMO 6 40 ab 40a 0 3245 1 2 HOMO 7 39 ab 39a 0 3325 1 2 HOMO 8 Cancel Back Next 4 3D Visualizer x Click on Next to proceed A progress bar is shown Progress orbitals 35 Stop Calculation Page 51 85 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 Severa
28. ate a table with the most important data Save as Excel v E ProjectList job_0000 job_0001 job_0001 job_SP_7 Y 5 TmolexProject job_GEO_1 Project Name TmolexProject TmolexProject TmolexProject TmoleXProject _Jjob_GEO_5 Job Name job_0000 job_0001 job_0001 job_SP_7 _ job_SP_6 job_SP_7 N Job_sP_8 2D structure gt 7 job_SCAN_9 v job_SCAN_11 o _ scan_0000 N scan_0001 Number of atoms 10 14 12 12 scan_0002 Basis functions def SV P def SV P def SV P def SV P J scan_0003 Charge 0 0 0 0 0 0 0 0 scan_0004 Multiplicity Singlet Singlet Singlet Singlet AE Freeze off off off off me Level of theory DFT Disp DFT D3 DFT Disp DFT D3 DFT Disp DFT D3 DFT b p scan_0006 Cosmo off off off off _scan_0007 Energy 135 062169 287 413943 194 204778 232 075794 _ scan_0008 Dipole moment 1 351271 eran anna Zero point vib ener 0 113743 0 104456 gt Additional results can be added to the table by selecting the jobs on the left side in the project list Page 85 85
29. ate is shown and can be changed as usual with dragging the mouse while keeping the left mouse button pressed TmoleXProject job 5 Bond Atom Style Labels p Edit additional label Translate Rotate b Scale Change torsion Copy Cut Delete Page 61 85 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 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 whenever such jobs are started 4 TmoleX 4 0 TmoleXProject acs X Fle Edit Templates Results Extras Tool Help 25 5 H 5 P Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 117 2 2046MB System 0 0 6296 2 MB v E ProjectList i Geometry Molecular Attributes Start Job Y E TmoleXProject i AAA ee
30. 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 A Edit x o 11272 y o 0 5254 Z l 0 8984 Charge oF Hybridisation custom A Saturate Amange J _Dekte Most entries can be changed in the fields Page 34 85 3 The 3D visualization Change the Element from H to C and also the Hybridisation to sp3 tetrahedral Objects Atom C 4 Atom properties Element al Edit AS y 0 5254 A z 0 8984 A Charge Tied por Saturate one bond a sp linear sp2 trigonal Molecules Aj sp2 lone pair sp3 lone pair a y moeaie v jl alcohols EXAMEN gt 1 but sp3d trigonal bipyramidal d 2 0r0 rad fartaihaderal Next click on Saturate to add missing hydrogens to the selected atom according to the given hybridisation Page 35 85 3 The 3D visualization 3 4 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 gt Objects Bond Atom C 1 J1 LAR C 4 ma Bond properties JN Type single r Length A 1 544 Guess Dihedral Angle
31. b panel and click on Run Page 55 85 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 2XPro 0 xX File Edit Templates Results Extras Tools Help 7 ty me 2 H 9 Open 3D Molecular Builder Jobs running local 0 4 remote 0 v E ProjectList h 5 TmolexProject Y job_GEO_1 Choose Job Template Charge gt Apply Job Template Y job_GEO_5 i EE Job Results Type of Calculation Single Point Calculation Status mos Converged SCF Convergence Open Viewer HOMO LUMO gap 5 139 eV Orbital Density Plot Status geometry Not performed Convergence Gradients Energy Vibrations Zero point VIBRATIONAL energy 0 0978161 Hartree Thermochemical Properties SCF energy 232 0765750 SCF E vibO 231 9787589 Population Properties NMR Shieldings View cosmo File Open Files ras _ Vibrational Modes Lo Energy __ _ _ Vibrational Spectrum A Moments mode mmetry wave number IR intensity selection rules i cm 1 km ps tas UV Vis Spectrum 1 0 00 0 00000 2 0 00 0 00000 HB co spectrum 4 0 00 0 00000 Ep tes Raman Spectrum Ey 0 00 0 00000 6 0 00 0 00000 ES IRSpectrum 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 ir 10 a 600
32. d 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 Fle Edit Templates Results Extras Tools Help laa fa k 25 H aw g Open 3D Molecular Builder Jobs running local 0 4 remote 0 v E ProjectList v 5 TmoleXProject e RA NPD COOP OOD OAL OL OA AOL EPL LO LLP POLL LOO ODDS OPT DEAL OTA L LOLOL TOR Y ee Choose Job Template Apply Job Template Y job_GEO_5 L Start Calculation Job type Method Geometry Optimization Ground state Level DFT Functional b p Spectra amp Excited States fofa bstona A e Tare ARI Single Point UV Vis and CD Vertical excitations Single Point Properties gt NMR shieldings Basis set def SV P Raman amp vibrational frequencies Potential Energy Scan PES Optical rotations dynamic polarizability Transition State Search Static polarizability Templates gt Batch processing gt Convergence Parameter Use resources Options Memory used for 500 0 Convergence criteria Disk 0 MB for HF No of CPUs 1 Gradient norm 3 dE dxyz 10 1 Hartree Bohr Max no of cycles 50 Delete scratch files after run Use internal redundant coordinates Save and Run Run local e rs Run network lt lt Previous Manage Job s Choose IR amp vibrational frequencies in the Start Jo
33. e 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 Measure Measure 3 87A v Delete Page 44 85 3 The 3D visualization 3 8 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 O or the key e to switch to rotation mode TmoleXProject job_notRun_3 Y S lo BOO Nix Rotation of the selected atoms can be done using x y z axis as rotation axis In addition to that the Page 45 85 3 The 3D visualization 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 Rotate tool x Pivot Xx 1 95 Y Pivot
34. e Saturate ANT UNO atom 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 T f dis ULA de ell E Ale View Edit Tool Display Type ES Save Export Coordinates Save to Fragment Directory Save Changes and Close Close This structure can then be used for modification or being saved in the user data base as described above Page 28 85 3 The 3D visualization 3 3 Easy building Paint tool A quite handy way to build is the paint tool File View Edit z e which can be chosen by clicking on the f 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 df lomaan pati li Be i Na Mg d K aK Rb sr KJ Cs Ba ff Hybridisation _sp3 tetrahedral tj X H 4 5 z 2lulpfulo Ssiile 6 jajn 79050 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 existi
35. e v Charge w Apply Job Template Y job_GEO_5 Y job_SP_6 esult Job Comparison Results Multiple Jobs Comparison Movie Y job_SP_7 Y job_SP_8 gt job_SCAN_9 Freeze None gt job_SCAN_11 gt job_TEMPLATE_14 Levelof theory rimmeetal 2011 b p Functional b p v Y job_BATCH_15 methylamine Export Files Save as Excel Y ethylamine A A A A A A A AE E E a a E A Y 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 A F liestas TmoleXProject_propylamine 16 0 0 Singlet 213 629261 0 825862 a roject e TmolexProject_aniline 14 0 0 Singlet 287 413943 2 052376 gt 3 TmoleXProject_p gt TmolexProject_ai E job_GEO_18 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 ln Tmolex ia 3 E cosmo COSMO files o E Ci J 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 77 85 8 Remote jobs 8 Remote jobs TmoleX as well as the client version of Tmol
36. eX 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 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 ME
37. eXProject job_notRun_3 x Number of atoms 9 Number of bonds 8 Objects multiple selected gt Angle 115 14 O smal fragment big fragment Page 37 85 3 The 3D visualization 3 5 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 TmoleXProject job_notRun_3 x Number of atoms 9 Number of bonds 8 gt Objects lt muttiple selected gt Bond properties Type single ail Length A 14312 Guess Length Guess Dihedral Angle E Freeze Bond Angle Scan Bond Angle Measure a N A Bond Atom Style Labels Edit additional label Invert selection Measure bond angle Molecules Atoms Y 4 Molecule Translate 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 x Number of atoms 9 Nu
38. els Atoms Show label 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 42 85 3 The 3D visualization Ji Bond Atom Style gt Edit additional label 7 Nu O er Select bond partners CJ Additional Substitute with b Change element r Coordinate gt o As connecting atom Arrange Saturate 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 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 Bond Atom Style Labels Edit additional label Translate Rotate Scale Create bond Merge overlapping atoms Add atom at center Create group Page 43 85 3 The 3D visualization o select two bonds measure angle Bond Atom Style Labels Edit additional label Translate Rotate Scale Scan freeze bond angl
39. 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 57 85 4 Properties For the calculation of nuclear shieldings choose this job type and simply run it 4 3 Nuclear magnetic shielding Start Calculation Job type Geometry Optimization Spectra amp Excited States gt Potential Energy Scan PES gt Transition State Search Single Point P Templates gt Batch processing P Single Point Properties gt IR vibrational frequencies UV Vis and CD vertical excitations NMR shieldings Raman amp vibra a 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 File Edit Templates Results Extras Tools Help 1176585 H 65 open 3D Mokcular Builder v E ProjectList Y 5 TmoleXProject Y job_GEO_1 Y job_GEO_5 Y job_SP_6 Y ES Manage Job s Jobs running local 0 4 remote 0 Saa Memory used for TmoleX 3 2 274 1MB System 0 0 6296 2 MB Choose Job Template Charge y Apply Job Template Job Results Scan job result Job Comparison Results Multiple Jobs Comparison Movie Type of Calculation Single
40. eometry 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 Convergence criteria Energy 6 101 Hartree Save and Run Gradient norm 3 dE dxyz 101 1 Hartree Bohr Run local 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 63 85 5 2 Use internal coordinates The job can then be started as usual also as a remote calculation A typical result is shown here 4 TmoleX 4 0
41. ermissions chmod a rx TmoleX linux _4 0 sh before starting it then follow the instructions on screen The full version of TURBOMOLE 6 6 is included in the TmoleX package Optimized binaries for a 32 bit Pentium compatible 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 TURBODIR 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 85 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 0 dmg To install Tmolex simply double click on TmoleX_macos_4 0 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 installati
42. es from a Huckel 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 70 85 7 Batch processing Generate batch jobs from existing jobs y Wi Projectuist Geometry Y E TmolexProject i Y job_GEO_1 Y job_GEO_5 Y Job Results Scan jo Y job_SP_7 Y job_SP_8 Type of Calculation Sin v job_SCAN_9 Z scan_0000 Y ESTO Y scan_0002 Y scan_0003 nergy Y zara naint VIBRATIONS Y scan_ Oot Export Results 4 Y scan_00l AA o 20 gt 3 job_SCAN_ k v job_TEMPLATE_14 Y job_0000 job_0001 v y job_BATC Jf methylamine Y ES Vibrational Modes Y propylamine Y aniiine 21a 10 2 a 11 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 Page 71 85 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 fi
43. ethod and basis set The NMR shieldings can also be displayed as labels in the viewer click on NMR Shieldings to open this view Page 58 85 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 gt Spectra amp Excited States IR amp vibrational frequencies Single Point P ROVNE Ae fini a citations NMR shieldings Raman amp vibrational frequencies Potential Energy Scan PES gt Optical rotations dynamic polarizability Transition State Search P static polarizability Single Point Properties gt 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 Unrestricted RPA Random Phase Approx No of excitations 5 TDA Tamm Dancoff Approx Unit nm o The spectra can be opened with the CD or UV Vis Spectrum button Open Files Output Energy Moments e EA fes CD Spectrum Bs Raman Spectrum es IR Spectrum Page 59 85 4 Properties 5 Constrained optimization and Scan jobs 5 1 Defining fixed internal coordinates TmoleX allows to define internal coordinates Bonds b
44. ettings 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 qsub is the default For LSF it should be bsub lt Page 82 85 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 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 Name of your run PBS N TmoleX job Number of nodes to run on PBS 1 nodes 1 Export environment PBS V 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 Tmo
45. f 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 4 TmoleX 4 0 TmoleXProject Emu File Edit Templates Results Extras Tools Help fa pp AS EH P Open 3D Molecular Builder Jobs running local 0 4 emote O Memory used for Tmolex 77 1 159 6 MB System 0 0 6296 2 MB y E ProjectList Geometr Atomic Attributes Molecular Attributes Start Job Y 5 TmoleXProject i KA T Choose Job Template w Charge Apply Job Template Level of Theory SCF Convergence Solvation Level Auxiliary basis sets for RI J DFT vy Use RI Element Basis set Auxiliary basis set G def SV P 2 v DFT settings def SV P H def SV P y Functional gpg def SV P Gridsize m3 v Activate COSMO Filename lt lt Previous Continue gt gt Manage Job s 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 i e DFT with empirical dispersion correction with or without RI J e MP2 lt 002 CCSD CCSD T spin scaled MP2 or CC2 calculation can also be used as sub options to the MP2 and CC2 level Page 18 85 2 A quick tour Settings for SCF convergence and special COSMO selections recomme
46. g 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 single jobs which are finished but not yet transferred back to your local desktop machine the icon switches to E F q DA EE Sen A fe job_BATCH_17 4 TmolexProject_meti 2 job_0 2 jobo 4 TmolexProject_ethy 2 jobo 2 jobo Y 7 TmolexXProject_propy job_0000 job_0001 Y TmolexProject_aniline job_0000 job_0001 Page 73 85 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 TmoleX settings PX Display settings Font type Font size 11 y File settings User directory C Users Tmolex Browse System 7 Available processors Total physical memory size 6296 2 MB Check memory Activate netbook option scrollbars Visibility of hydrogens in export table Default with hydrogens without hydrogens TURBOMOLE Defaults Optimization Settings Energy con
47. ied 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 4 TmoleX 4 0 TmoleXProject File Edit Templates Results Extras Tools Help a a E 5 open 3D Molecular Builder Jobs running local 0 4 Cicle 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 Paar top Potential Energy Scan PES Potential energy scan Transit ee ne Basis set def SV P Symmetry C1 Templates gt Convergence Parameter Batch processing gt Energy 105 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 g
48. ify or apply Templates x Choose Template Load template Choose Job Tempete _ New Template Job1 X lt _ ee E Put ae ee Settings ae Y Turbomole Mopac w i ee Turbomole A Geometry Symmetry Check 0 0010 max allowed deviation during check Bohr Atomic Attributes Basis set def Sv P y Molecular Orbitals Molecular charge 0 0 Multiplicity Singlet UHF z Freezing point Hartree 9 99999999E8 for post HF in Hartree Method Level DFT Y R URI Functional BP86 y Gridsize m3 v Dispersion SCF convergence COSMO settings Max number of SCF iterations 30 COSMO On conv criteria SCF energy 10 7 Hartree Epsilon SCF density 1d 7 Example 1 0d 8 Job type Job Type Geometry Optimization Ground state v Max no of cycles 50 L Use internal redundant coordinates Your choice Close Save as Template Apply Template The settings are quite self explaining Page 65 85 Create new job template Click on 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 6 Job Templates 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
49. installation directory on the target system The 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 whether 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 Configuring a remote system such that number crunching programs like TURBOMOLE can utilize the hardware resources correctly is not a trivial task Most Linux Unix systems restrict the permissions for memory or disk space for each individual user for security reasons TmoleX is able
50. l properties can be displayed in the same window Check the memory usage of TmoleX from time to time when using this option 3D Visualizer Open the Viewer with the Following Property Choose orbital F Sym Energy Har La E HOMO LUMO 50a 0 0213 LUMO 2 49a 0 0607 LUMO 1 48a 0 0869 LUMO 0 2229 HOMO 46a 0 2253 HOMO 1 45a 0 2378 HOMO 2 Choose property to view Open in New Window Generate New Property Page 52 85 3 The 3D visualization File View Edit Tools Display Type Window Help N SA VISUC atiC TmoleXProject job_GEO_5 plot 47a HOMO x Number of atoms 21 Number of bonds 21 gt 00000 o _left mouse button Click or drag to select right mouse button rotate MMB move wheel zoom 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
51. lation TmoleX is available in your Windows Start Menu or as an icon on your desktop Please Note TURBOMOLE 6 6 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 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 The parallel MPI version is only functional on Windows systems with an installed version of MS MPI Please download and install MS MPI from the Microsoft website search for HPC pack MPI and download mpi_ x64 msi Page 5 85 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 0 sh Please make sure that the file has execute p
52. leX 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 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 83 85 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 jobs are of course added by TmoleX automatically 4 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 E
53. les is zero Geometry gt gt GEO OPT quick xmil Charge Apply Job Template ES Y All settings for basis set method job type etc can not be changed in batch jobs since they are defined in the job template 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 _ Atomic A Oo 5 cular A od Start Job GEO OPT quick xml Charge yhy 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 job1 job 2 C YUsers TmoleX COSMOJOGICA dd ata is 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 a Charge used from input used from input 14 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
54. mber of bonds 8 gt Objects multiple selected gt Change bond angle Angle 117 538 O small fragment big fragment POS Nix Molecules Atoms v Molecule Y 1 alcohols J 1 butanol sdf Page 38 85 3 The 3D visualization 3 9 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 Ly TmoleXProject job_notRun_3 x Number of atoms 9 3 Y Objects Atom H 7 Atom properties Bond Atom Style Label Element H Edit additional label X re Translate y gt Select bond partners Z A alcohos gt a Change element gt amino_acids Hybridisation custom Coordinate gt carbonyls b As connecting atom hydrocarbons gt A O Arrange misc gt Saturate pah 7 b Paste rings de anes Molecules Atoms Y Molecule Cut OH k v Y alcohols Delete 3 d 1 butanol sdf C N 2 propenol sdf CE NO2 gt Attach with custom atom Open to edit sdf Mil methanol sdf J tert butanol sd gt 4 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
55. molecule for which input coordinates exist e g benzene The buttons t ip 5 Import Coordinate File 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 Open Coordinate File Look In rings BE benzene sdf F benzimidazole sdf 2 borazine sdf Fi imidazole sdf Ri indole sdf 4 pyrazole sdf 4 pyrrole sdf PX pyrrolidine sdf 4 thiophene sdf File Name benzene sdf Files of Type all coordinate files Open Cancel Select the coordinate file and load the molecular structure of benzene into TmoleX first change to the installation directory COSMOlogic Tmolex14 COSMObuild fragments rings Alternatively klick 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 gt i MISC gt Ww pah Y J rings Mi benzene sdf benzimidazole sdf borazine sdf Page 11 85 2 A quick tour 2 3 The tool bar pp AN H 7 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 i e which is opened in the project list pa Create new job within the current project ya Create new batch job within the current project Tag Read or import coordinate
56. ms 12 Number of bonds 10 a Objects multiple selected gt Translate tool o SEXAN W carbonyis gt dy hydrocarbons gt Wy misc gt de pah gt Wy rings Y 4 smal_common J1 ch4 sdf Ml h20 sdf h2s sdf hen sdf nh3 sdf nitro sdf 00000 a e 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 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 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 Page 47 85 3 The 3D visualization e Finally the scale tool gt key r scales or resizes relative distances between a
57. nd 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 will 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 24 85 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 Results ExtraggsTools Help C li liar i H 89 Open 3D Molecular B de Y E ProjectList Y 5 TmoleXProject Y job_GEO_1 job_notRun_2 Jobs running local 0 4 remote 0 Atomic Attributes Molecular Attributes aM Charge Coords amp Sym _ 35 Import Coordinate Fie 82 Open 3D Molecular Builder UNIS Aw Atomic symmetry Number of atoms 0 Current point group C1 Max tolerance 0 001 au Autodetect Symme New Atom New point grou Point group C1 Apply New Point Grc The molecule builder can be used most conveniently by starting
58. nded only for expert users can also be found in the method section Atomic Attributes Molecular Geometry Choose Job Template Charge Level of Theory SCF Convergence Solvation SCF convergence parameters Energy convergence 10 Hartree 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 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 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 increased See the TURBOMOLE manual for details about DIIS Page 19 85 2 A quick tour 2 5
59. ng atom to replace it with the selected atom fragment Click on the hydrogen Page 29 85 3 The 3D visualization 3 4 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 Measure distance a Invert selection 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 30 85 3 The 3D visualization To merge two fragments which are not just connected by one bond a more powerful 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 Ji PivotatCoM A Leal LN View Page 31 85 3 The 3D visualization 11 create a bond between two atoms select it and change its length to zero D I A Bond Atom Style
60. on and extend the PATH to STURBODIR scripts and STURBODIR bin sysname the binary directory 1 4 Online Updates TmoleX 4 0 now 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 Monthly Never install4j Next gt Cancel Page 7 85 1 Installation Page 8 85 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 ProjectList Welcome to TmoleX Version 20 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 caled TmoleX_Project in your home folder Please choose one of the following options New Project 2 Open Project Online Videos How To Tmolex Documentation m Manage Job s 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 85 2 A quick tour All projects will require a new di
61. ond 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 TmoleXProject job 5 Bond Atom Style b Label Edit additional label Measure torsion 4 Guess length Guess dihedral angle On the right the options for freezing a bond length are show To delete constraints select here and delete Objects Constraint stre C1 C3 v Constraints Constraint stre C1 C3 Y Delete Constraint Length A 15249976 __To scan along the coordinate activate the Mark for scan lt check box and set minimum maximum and mn TE ad the step width not the number of steps Maximum 1 525 Current step size 0 Page 60 85 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 E TmoleXProject job 5 LA Bond Atom Style Labels Edit additional label Invert selection Measure bond angle Translate Rotate Scale Change bond angle Swap bonds Copy Cut Delete 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 coordin
62. otal energies for the optimization steps can by viewed here ESS EOR lt Fie View Edit Tool Display Type Window Help a Q a a a KA 0 Q a Gradients Vib Modes J Internal Coords Builder orbital viewer a Scan TmoleXProject job_GEO_5 gradient _ x number of atoms 21 Number of bonds 21 gt Arro visible Arrow Energy 647 4871 64 7844338 O Calculate bonds 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 stepwise back and forth Page 49 85 3 The 3D visualization 3 10 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 D 15658 E 6 9 open 3D molecular Builder Jobs running local 0 4 remote 0 v E ProjectList Y 5 TmoleXProject Y job_GEC_1 ola Memory used for noes SLEE saeni 006298218 Choose Job Template Charge Y Apply Job Template Status mos HOMO LUMO gap Status geometry Converged Geometry Convergence Criteria convinfo energy change actual value 0 7690E 07 threshold 0 1000E 05 geom gradient actual value 0 1889E 04 threshold 0 1000E 02 Energy
63. ow MASSUTE ld ree bonds Ls f pS a ps ho TmoleXProject job_notRun_2 Molecules Atoms r Y 4 Molecule Y 4 alcohols 1 butanol sdf 1 2 propenol sdf ethanol sdf a p sdf Mido sdf isopropa vol menan i le e amino aE e lo rarhanide gt A d d d d Es o aas 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 Xp General Molecule Labels COSMO cavities Properties Path Fragments eee Settings Database SMOlogicAppData TmoleX14 fragments Browse Scan depth 232 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 contains 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 Page 27 85 3 The 3D visualization e the second line can contain the name of the fragment the way it will be displayed in the Molecules section of the builder The replacement atom can be chosen with the right mouse button menu Bond Atom Style Label Edit additional label Translate Select bond partners p Substitute with Change element p Coordinate F Arrang
64. pe of Calculation Geometry Optimization Status mos Converged SCF Convergence jewer HOMO LUMO gap 5 139 eV Orbital Density Plot Status geometry Converged Convergence Gradients Geometry Convergence Criteria convinfo energy change actual value 0 7690E 07 threshold 0 1000E 05 geom gradient actual value 0 1889E 04 threshold 0 1000E 02 Energy g E Open Files totalenergy 232 07657502616 IEA Output kinetic energy 229 29023106507 potential energy 461 36680609123 Energy Moments Gradients Bs cyde 1 SCFenergy 232 0757937330 dE dxyz 0 018796 ta cyde 2 SCFenergy 232 0765545974 dE dxyz 0 003180 cyde 3 SCFenergy 232 0765749475 dE dxyz 0 000173 ps cyde 4 SCFenergy 232 0765750244 dE dxyz 0 000064 What next Start new job with current data as input Save as job template for further usage lt lt Previous Manage Job s Important a Check the Status of the molecular orbitals and the status of the geometry optimization 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 If the geometry is not converged restart the optimization allowing more geometry cycles 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 P
65. possible e g 2 derivatives for post Hartree Fock methods are not supported by TmoleX COSMO calculations and frequency analysis is not supported either etc Defining multiple jobs in one job template will tell TmoleX to run them one after the other using the coordinates of the preceding step Use final coordinates j i Use final coordinates Use final ona job 1 of job 1 job 2 of job 2 p job 3 of job 3 A typical work flow would be RI DFT geometry optimization 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 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 inp
66. r Ao Y job_GEO_1 Choose Job Template Charge Y Apply Job Template Y job_GEO_5 Y job_SP_6 Start Calculation Y job_SP_7 Y job_SP_8 Job type Method E Geometry Optimization gt Ground state Leva mil Functional b p Spectra amp Excited States gt Single Point gt 2 Basis set def SV P Symmetry C1 Single Point Properties gt Potential Energy Scan PES gt nergy 10 Transition State Search gt i 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 O 3 dE dxyz 10 Hartree Bohr Delete scratch files after run Max no of cycles 50 4 Use internal redundant coordinates AA 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 62 85 5 2 Use internal coordinates 5 4 Scan along an internal coordinate The potential energy scan PES method can be appl
67. r Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 95 0 159 6MB System 0 0 6296 2 MB v E ProjectList Y 5 TmolexProject job_notRun_1 Start Job Atomic Attributes Molecular Attributes Choose Job Template v Charge v Apply Job Template Start Calculation Job type q Method Geometry Optimization Ground state Level oT Functional b p Spectra amp Excited States Mic Single Point UV Vis and CD vertical excitations NMR shieldings Basis set def SV P Symmetry C1 Raman amp vibrational frequencies Optical rotations dynamic polarizability Single Point Properties gt Potential Energy Scan PES p Convergence Parameter Energy amp Density Transition State Search P Static polarizability hn Templates gt Batch processing gt Use resources Memory used for 500 0 MB Opti ee Disk 0 MB for HF Convergence criteri No of CPU O Ol s 1 Energy 6 101 Hartree E radi 1 Ld Delete scratch files after run Gradient norm dE dxyz 10 Hartree Bohr Max no of cycles 50 Save and Run L4 Use internal redundant coordinates Run local Save Run network lt lt Previous Manage Job s 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 U
68. rangement 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 7 which is included in the default installation of TmoleX EEN The MOPAC7 button will open a new window with several options Transition State Search Charge O Read Restrictions Show run status Start Calculation Stop Calculation Ready to start Mopac optimization AM1 PM3 MNDO MNDO 3 are the available methods they all are parametrized for a certain number Page 41 85 3 The 3D visualization 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 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 Viewer options Ex Path Grid Misc COSMO cavities Properties General Molecule Lab
69. rectory 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 L jchempaint lx Links Contacts Lo Music il CosMOlogic E Pictures J COSMOlogicAppDatal1 Searches L COSMOthermX12 M fimoexProiect Mi Desktop F Documents la Downloads El Favorites File Name C Users Tmolex TmoleXProject Files of Type 5 iw i ta 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 File Edit Templates Results Extras Tools Help v E ProjectList Y 5 TmoleXProject Choose Job Template Y Charge H Open 3D Molecular Builder Jobs running local 0 4 Atomic Attributes _ Molecular Attributes Method v Apply Job Template gt S Results Coords amp Sym i Import Coordinate File Pp Open 3D Molecular Builder Atomic l Symmetry Number of atoms 0 New Atom Current point group C1 Max tolerance 0 001 aU Autodetect Symmetry New point group C1 g Apply New Point Group Internal coordinates Page 10 85 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
70. s Charge Multiplicity Freeze Level of theory Cosmo Energy Dipole moment Zero point vib energy job_0000 job_0001 TmolexProject TmoleXProject job_0000 job_0001 L L 12 12 def SV P def SV P 0 0 0 0 Singlet Singlet off off DFT Disp DFT D3 BJ damping Grimme et al 201 DFT Disp DFT D3 BJ damping Grimme et al 201 off off 194 204778 194 204778 1 526881 0 104456 Here an example of ethanol the job template was GEO OPT from the predefined list of job templates Page 68 85 7 Batch processing 7 Batch processing The job templates described in the previous chapter can easily 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 Gx File Edit Templates Results Extras Tools Help a 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 gt b J Y 5 TmoleXProject j 2222 A Y job_GEO_1 Choose Job Template v Charge Apply Job Template TO Y job_GEO_5 Y job_SP_6 Coords amp Sym Multiple Coordinates Y job_SP_7 Y job_S
71. s besides TURBOMOLE also many different formats Yi 15 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 0 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 1MB_ System 0 0 6296 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 85 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 on the top the general task menu Geometry Atomic Attributes Molecular Attributes etc 3 in the main frame the data assigned to the chosen task 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 Start Job gt Results after a succes
72. 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 Ly button Page 39 85 3 The 3D visualization Alternatively any other atom can be used as connecting atom Objects Atom H 7 Atom properties Bond Atom Style ad Edit additional label aie Translate 0 394 Select bond partners ian FETT Ihe wi ae Substitute with ds CH2 4 OH gt Change element Coordinate As connecting atom Arrange Saturate 2 propenol gt Yordisatio custom ethoxy Saturate Arrange geranyl Paste Copy Cut Delete 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 40 85 3 The 3D visualization 3 6 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 Saturate all Re compute bonds Set name Set fragment name Unset connect atom A simple rear
73. se resources part can be used to set maximum amount of memory RAM and disk space 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 21 85 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 gt A o o abr IA ar 4 TmoleX 4 0 TmoleXProject EX File Edit Templates Results Extras Tools Help b o om H 5 4 Open 3D Molecular Builder Jobs running local 0 4 remote O Memory used for TmoleX 129 2 195 7MB System 0 0 6296 y E Projectlist Atomic Attributes Molecular Attributes Y 3 TmoleXProject Mg job_GEO_1 Choose Job Template v Charge Apply Job Template Job Results E O O Ty
74. sful 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 13 85 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 create internal coordinates add atoms or modify the structure e TmoleX 4 0 TmoleXProject Gl es File Edit Templates Results Extras Tools Help 7 IG ES gS EH P Open 3D Molecular Builder Jobs running local 0 4 remote 0 Memory used for TmoleX 87 6 151 5 MB System 0 0 6296 2 MB Y E ProjectList Method Statlob gt Results Y E TmoleXProject a O a a ERAS Choose Job Template v Charge Apply Job Template gt gt Coords amp Sym 25 Import Coordinate File 89 Open 3D Molecular Builder Os as Atomic Symmetry Internal coordinates Number of atoms 12 a Current point group C1 Constraints Value Max tolerance 0 001 3U Autodetect S
75. t system for all jobs e total avail CPUs the total number of CPUs on that system Helpful for the workload check see below Server IP Work directory TURBOMOLE directory Use max CPU total avail CPUs total avail RAM MB tmolex 10 0 0 205 10 0 0 205 home tmolex Tm software TURBOMOLE tmolex 10 0 0 208 10 0 0 208 scr tmolex Projects software TURBOMOLE tmolex 10 0 0 250 10 0 0 250 home tmolex Tm software TURBOMOLE tmolex 10 0 0 250_g and home tmolex Tm software TURBOMOLE Check workload Delete Machine Hint To add new remote systems just submit a job to the remote machine and save the settings just before starting the job 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 75 85 7 Batch processing current 45 min ago 15 m n ago available CPUs 2 96 1 99 0 93 l4 Show expert informations top 16 27 49 up 7 min 5 users load average 2 96 1 99 0 93 asks 152 total 4 running 148 sleeping O stopped 0 zombie Cpu s 44 1 us 1 1 sy 0 0 ni 50 72id 4 0 wa 0 0 hi 0 0 si 0 0 at Mem 6116176k total 2667364k used 3448812k free 18440 buffers Swap 8393920k total Ok used 8393920k free 18 831400k cached PID USER PR E VIRT BES SHR 5 CPU MEM TIME COMMAND 5001 tmolex z0 o 2477m 646m 595m
76. ter2 xyz A out_12 xyz EC_25112007 sdf Jout_13 xyz irgendeines cosmo out_14 xyz job_BATCH_33 cosmo out_15 xyz job_BATCH_33 energy out_16 xyz Aleflunomide_1 xyz M1 out_17 xyz A out_0 xyz A out_18 xyz CA out_1 xyz MI out_2 xyz amines sdf File Name Files of Type _ all coordinate files Fie Edit Templates Results Extras Tools Help v E ProjectList Y 5 TmolexProject Y job_GEO_1 Y job_GEO_5 Y job_SP_6 Y job_SP_7 Y job_SP_8 gt 3 job_SCAN_9 gt 3 job_SCAN_11 gt 3 job_TEMPLATE_14 I methylamine E ethylamine propylamine aniline Manage Job s 3 fa a omy H Ge 9 open 30 Molecular Builder 4 Jobs running local 0 4 remote 0 Memory used for Tmolex System 0 0 6296 2 MB Atomic Attributes Molecular Attributes Method SY Startlob gt Results Choose Job Template Y Charge A Apply Job Template 3 Coords amp Sym Multiple Coordinates Te add Molecule 2 Delete Molecule Number Name Charge Image click to view modify 1 methylamine 0 2 ethylamine 0 3 propylamine 0 4 aniline 0 Apply Job Template amp Prepare to Run 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 determin
77. 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 Page 80 85 8 Remote jobs 8 3 Start a remote job Starting jobs can be done by choosing a machine in the list of saved systems Set Parameter for external Job ES Note runs only on Linux Unix systems Select settings tmolex 10 0 0 205 Data for remote system Server IP 10 0 0 205 max total number of CPUs User tmolex number of CPUs in use Password ETTET Check workload Check Password Settings Configure Work directory home tmolex Tmolex_Jobs TURBOMOLE directory software TURBOMOLE_66 TURBOMOLE Number of CPUs for job s 1 Check every 1 min Check remote system Use queuing system Delete Settings Clear Add New Load Settings 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 Y aniline 12 job_SCAN 11 GEO
78. toms Add a benzene ring select it and use this tool to see what it does 3 9 The gradient viewer Once you have completed a geometry optimization you can open the gradient viewer from the results panel Fie Edit Templates Results Extras Took m fy aw lo H PS 2 Open 3D Molecular Builder v E ProjectList Y Gs TmolexProject Y EN Memory used for Tmolex System 0 0 6296 2 MB v Apply Job Template Type of Calculation Geometry Optimization Geometry Convergence Criteria Status mos HOMO LUMO gap Status geometry Converged Converged Convergence convinfo energy change actual value 0 7690E 07 threshold 0 1000E 05 geom gradient actual value 0 1889E 04 threshold 0 1000E 02 Energy totalenergy 232 07657502616 229 29023106507 potentialenergy 461 36680609123 Vibrations Thermochemical Properties Population Properties NMR Shieldings View cosmo File Open Files SCF energy 232 0757937330 dE dxyz 0 018796 SCF energy 232 0765545974 dE dxyz 0 003180 SCF energy 232 0765749475 dE dxyz 0 000173 SCF energy 232 0765750244 dE dxyz 0 000064 Output Energy Moments la UV Vis Spectrum las CD Spectrum las Raman Spectrum ls IR Spectrum What next Start new job with current data as in Save as job template for further usz Page 48 85 3 The 3D visualization The t
79. total energy 232 07657502616 kinetic energy 229 29023106507 potential energy 461 36680609123 SCF Convergence 5 139 eV Convergence 232 0757937330 dE dxyz 0 018796 232 0765545974 dE dxyz 0 003180 232 0765749475 dE dxyz 0 000173 232 0765750244 dE dxyz 0 000064 Open Viewer Orbital Density Plot Gradients Vibrations Thermochemical Properties Population Properties NMR Shieldings View cosmo File Open Files o creencias A A Moments las UV Vis Spectrum ls CD Spectrum ls Raman Spectrum las IR Spectrum What next Start new job with current data as in Save as job template for further usz Page 50 85 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 3D Visualizer What do you want to visualize a orbitals Density total spin MP2 excited state derivates response Electrostatic properties potential field field gradient Quality Reduced resolution quick Normal resolution slow For most users the molecular orbital will be of most interest Select occupied or unoccupied orbitals and proceed with next to the calculation Mark a list of orbitals the Occupation helps to distinguish occupied and virtual orbitals the last column counts the occupied orbit
80. ut 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 KA ENE SEATA ES E idl 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 Run network The job can either be started on the local system or submitted to a remote machine using the Run network button Page 66 85 6 Job Templates 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 sro x i File Edit Templates Results Extras Tools Help 5 ii la a EH amar g Open 3D Molecular Builder Jobs running local 1 4 remote 0 Memory used for Tmolex __176 8 275 6 MB System 500 0 6296 2 MB vE ProjectList Atomic Attributes gt Molecular Attributes gt Method Results ES T molexProject i a Y job_GEO_1 OPT FREQ xml w Charge Apply Job Template Y job_GEO_5 Y job_SP_6 Jobs Y job_SP_7 Y job_SP_8 ID Type Start Stop Y 7 job_SCAN_9 GEO DFT RI B P charge 0 c1 def SV P GE Jun 2 2014 4 06 53PM Jun 2 2014 4 07 30 PM Y scan_0000 GEO DFT Disp RI charge 0 C1 def SV P Jun 3 2014 9 47 47
81. vergence 6 Gradient norm 3 Max no of cydes 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 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 F Delete scratch files after run Page 74 85 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 y j a A X40 mole Pro LE i L A A A Er k File Edit Templates Results Extras Tools Help Y E ProjectList 5 TmolexProject Y job_GEO 1 this will open eS Server IP Work directory TURBOMOLE directory Use max CPU total avail CPUs total avail RAM MB tmolex 10 0 0 205 10 0 0 205 home tmolex Tm software TURBOMOLE 0 tmolex 10 0 0 208 10 0 0 208 scr tmolex Projects software TURBOMOLE 0 tmolex 10 0 0 250 10 0 0 250 home tmolex Tm software TURBOMOLE 0 tmolex 10 0 0 250 q 10 0 0 250 home tmolex Tm software TURBOMOLE Hint To add new remote systems just submit a job to the remote machine and save the settings just before starting the job There are two entries e Use max CPU the total number of CPUs TmoleX is allowed to run on tha
82. ymmetry New point group Cl Apply New Point Group New Atom Delete Selected Atoms Number Element Fixed cartesian Fixed internal DO Y DUN Aa YN TIT ZDZDA A aaa SC S oO O O O O O O O A O Continue gt gt Manage Job s Page 14 85 2 A quick tour 2 5 2 Basis set panel The basis set is being defined in the Atomic Attributes panel File Edit Templates Results Extras Tools Help 0 D Se GS E 65 9 open 3D molecular Builder Jobs running local 0 4 remote 0 Memory used for Tmolex 92 9 151 5MB System 0 0 6296 2 MB v E ProjectList Geometry Atomic Attributes Method Y E TmoleXProject job_notRun_1 Results Nuclear ch Basis Set for all Atoms def SVP def SV P 12 0110 def SV P 12 0110 def SV P 12 0110 def SV P 12 0110 def SV P 12 0110 def SV P 12 0110 def SV P 1 0079 def SV P 1 0079 def SV P 1 0079 def SV P 1 0079 def SV P 1 0079 def SV P 1 0079 m Basis for elements o ShowEP _ j C defsviP O oy H def SV P z O ONDUA YN pr o m n z 2 z z z z injana pi p j pd Ad OO aO aO aO VD p N Basis for individual Atoms Select items from table or graphic viewer Choose Basis Sets Continue gt gt 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

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