COSMOconfX User Guide
Contents
1. Making your own job definition sessssesssseseeeseeee eene enne nennen nnn 16 4 1 The COSMOconf WOTKTIOW vies cexdsansoedenlagotideuhaduete Feba ud ep tte tiet Reese de qe tte debs deese teen 17 2 2 IJnmtoperatioris7 Steps aste ema i toad deleeo ded esu dace e Sa oto dudes 18 1 Quickstart 1 1 Introduction This document will guide you through a standard COSMOconf calculation i e a calculation using a pre defined job template In our example we will use the BP TZVP COSMO template for the creation of conformer COSMO files that can be used with the BP TZVP parameter ization of COSMOtherm 1 Create a project File Edit Run Extras Help 7 s m e Project List The project directory existing directory has to be selected in the file chooser A new project directory this is the name of our new project can be added to the path In the above example we create the project First project Look in amp s Tz c COSMOconfProject Folder name C CC_Files Project First_Project wsm I sena cen 2 Load molecules Select the new project just click the project in the list and click the Load molecule s button Running Jobs Now use the file chooser to load the structures of interest In our case this is aspirin xyz eth anol xyz and glycerol xyz The reader accepts the structure file types of th2. http users abo fi mivainio balloon Mikko J Vainio and Mark S Johnson 2007 Generating Con former Ensembles Using a Multiobjective Genetic Algorithm Journal of Chemical Information and Modeling 47 2462 2474 Table 1a Parameters of calculation types given in table 1 Parameter tag Description Default AM1 PM3 GAS AM1 PM3 COSMO AM1 PM3 COSMO SP n batch number of MOPAC calculations per batch divide the multi 1000 step job into n batch batches CF MOPAC CONF GEN max gas opt maximum number of MOPAC gas phase calculations in first 5000 step cf generator method defines the cf COSMOfrag keywords for the conformer gen 2 eration in the first step of the procedure 0 simple method action 3 1 method 2 but less angles per bond rotation rotconf crude action 3 2 includes rotations of important bonds rotconf action 3 3 method 2 but more angles per bond rotation rotconf fine action 3 23 cf enable rotalk enable disable rotation of alkyle chains O off 120n n batch number of MOPAC calculations per batch divide the multi step job into n batch batches 1000 BALLOON CONF GEN options The base options always used are verbose 0 forcefield MMFF94 mff fullforce 1 ninitialDimensions 6 maxtime 200000 nobadmodels 1 expand 1 contract 1 pStereoMutation 0 00 Other keywords will be added to the upper ones
3. CACC FilesMy Results Dateityp siechen I of an output set will be treated as conformers and numbered in the order of ascending energies The name of the job will be used as base name of the conformer files E g the cosmo conformers of an aspirin job will be sorted and renamed to aspi rin c0 cosmo aspirin cl cosmo etc The same holds for energy files If the rename option is switched off the files will be copied without renam ing i e the names of the output sets will be used 14 2 8 The job status section This panel gives a synopsis of the running and finished jobs of a project In our example we have three finished and one running jobs all on the local machine q m ID Name Start Stop No of CPU Machine aminol Dec 17 2012 12 30 04 PM Dec 17 2012 1 01 50 PM Local 1 ethanol Dec 18 2012 2 54 19 PM Dec 18 2012 2 55 58PM 1 Local ipazine Dec 18 2012 2 55 58 PM Dec 18 2012 4 16 22 PM 1 Local aceticaci Dec 18 2012 4 35 38 PM Running 1 Local Wi 3 COSMOconf Linux command line version All features of COSMOconf can be used from the command line to enables full batch pro cessing capabilities In addition a command line installation on a Linux computer is necessary to submit remote calculation from the GUI 3 1 Installation Linux A TURBOMOLE installation version 6 4 or higher is required for COSMOconf to work cor rectly Installation To en
4. creation lt info gt lt just a name used in the output error messages gt lt file of output molecule set not needed for input gt molecule set_out gt step2 out xml molecule set out lt method string of calculation gt lt method gt CLUSTER GEODIS lt method gt lt options gt valuc lt optiuons gt lt status waiting running ready gt lt status gt waiting lt status gt lt error gt number 0 number lt message gt lt message gt lt error gt lt step gt lt job_schedule gt lt job gt Step 2 20 Table 1 Implemented steps Acronym Description QM calculation AM1 GAS AM1 gas phase optimization MOPAC7 AM1 COSMO AM1 COSMO optimization MOPAC7 AM1 COSMO SP AM1 COSMO single point calculation MOPAC7 PM3 GAS not tested PM3 COSMO not tested PM3 COSMO SP not tested BP TZVP COSMO BP TZVP COSMO optimization TM BP TZVP GAS BP TZVP gas phase optimization TM BP SVP COSMO SP BP SVP COSMO single point TM BP SVP GAS SP BP SVP gas phase single point TM BP SV_P COSMO LOOSE BP SV P cosmo optimization with quite loose conv crit TM BP SV_P GAS LOOSE BP SV P gas optimization with quite loose conv crit TM BP TZVPD GAS SP BP TZVPD single point gas phase calculation for COSMOtherm FINE level TM BP TZVPD FINE COSMO SP BP TZVPD single point COSMO cal
5. please visit http sourceforge net projects mopac7 2 TURBOMOLE a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 http www turbomole com 16 gas phase energies Therefore the gas phase structure of conformer name cO energy does not necessarily correspond to the COSMO conformer structure name cO cosmo Restart The calculations can be restarted by using the same command in the same start directory COSMOconf examines the already existent files and decides what to do 3 4 Example The following scheme explains the creation of COSMO files on the BP TZVP COSMO level 1 Create 3D input structures e g XYZ files 2 Create a directory and copy the 3D files into this directory e g mkdir new calc cd new calc copy the filesto new calc 3 Create a list of the input file names the file is called list hereafter Content of the file list ethanol xyz methanol xyz water xyZ 4 Start the script cosmoconf pl 1 list m BP TZVP COSMO gt list log The output of the script can be found in the file List log The COSMO files are collected inthe Results of job BP TZVP COSMO directory 4 Making your own job definition COSMOconf features a fully configurable calculation workflow to enable user defined calcu lation schemes To efficiently use of these features some knowledge about xml and the dif ferent quantum chemistry levels as well as a funda
6. a via the options tag E g options nconfs 90 nGenerations 99 RMSDtol 0 2 options The options have to be separated by a semicolon b default empty or missing option tag a series of 7 balloon jobs will be used 1 randomSeed 7 nconfs 100 noGA 1 2 randomSeed 1 keeplnitialz1 nconfs 100 nGenerations 20 RMSDtol 0 1 pTorsionMutation 0 5 noPopulationGrowth 1 3 randomSeed 2 nconfs 100 nGenerations 100 RMSDtol 0 2 pTorsionMutation 0 2 noPopulationGrowth 1 4 randomSeed 3 nconfs 100 nGenerations 200 RMSDtol 0 3 pTorsionMutation 0 1 5 randomSeed 4 nconfs 100 nGenerations 500 RMSDtol 0 4 6 randomSeed 5 nconfs 50 nGenerations 1000 RMSDtol 0 5 7 randomSeed 6 nconfs 50 nGenerations 1000 RMSDtol 0 6 The structures of all steps will be accumulated see left CLUSTER_GEODIS geodis threshol d1 conformers with a geodis value smaller than geodis thresholdl will be considered as equal 0 5 d2 geodis threshol conformers with a geodis bigger smaller than 2 0 24 geodis threshold2 will be considered as different dihedral threshold conformers with a geodis value between the upper bounds 10 0 will be checked by a local dihedral angle comparison This is the max allowed deviation in degrees CLUSTER EVNN e clust thresh energy window in kcal mol 0 05 k
7. job step can be viewed changed by using the View SET PA RAMETER button Already defined steps can be changed via the right mouse button menu This can also be used to modify the predefined default procedures Number Name Method Status 1 Noname s N waiting 2 Noname R Change method EC waiting 3 Noname S Add step gt waiting No name ci Delete step waiting 5 _ Noname R OTe waiting The user defined procedures can be saved SAVE AS TEMPLATE and used as USER TEMPLATES af terwards Another way to define a new job template is the use of the Ebit gt EDIT TEMPLATE option of the menu bar Here you can find an option for the deletion of a user defined job Because the job definition is used to store the status of the single steps it cannot be changed for running or finished jobs 2 5 Running jobs locally or remote Local jobs jobs on the local machine can be started without further settings The only pa rameter that can be changed is the number of CPUs that should be used see EXTRAS gt SET TINGS This number defines the maximal number of jobs running at the same time Surplus jobs will be queued Because the work environment of a remote Linux system cannot be 12 known by the GUI the user needs to define the settings The settings for a machine can be saved SAVE SETTINGS at the bottom of the menu and re used SELECT SETTINGS In order to check the password and login we re
8. use of COSMOfrag and MOPAC for the initial con former generation These are included for smaller molecules and compatibility to 11 previous versions All templates not containing a MF will use BALLOON as a conform er generator Job Definition There are two ways to define the procedure that should be used The easiest and recom mended way is the use of a predefined procedure which can be chosen from the DEFAULT TEMPLATES lists fa ethanol e Start Set Job Definition Gasphase Templates v COSMO Templates z Gasphase COSMO Templates X User Templates Y OSMO Templates BP SVP AM1 COSMO Used Template Info BP SVP AM1 MF COSMO P Add Ste Save as Template 2 Run This Job local Run This Job network see or vp cosuo Number MetnqBP TZVP MF COSMO Status MoleculeSetOut Error Error message Parameter BP TZVPD FINE COSMO A more advanced option is the individual set up of the procedure The GUI allows for user defined job definitions which can be stored as UsER TEMPLATES with the SAvE As TEMPLATE but ton More details on modifying templates can be found in the making your own job defini tion section of this manual The jobs steps can be added with App Step button which offers steps of different types ster ion A aa Sup Conformer Generation gt Cluster LI Reduce gt QM Job gt Other The position of a step in the job can be changed with the blue arrows tA w The parameters if existent of a
9. D HERE lt METHOD gt XPARAMETER TAG gt PUT THE PARAMETERS HERE lt PARAMETER TAG step 19 Example Job definition XML lt xml version 1 0 encoding 1580 8859 1 general remarks error number 0 gt normal termination error number 0 gt error the error message should contain some description of the problem job error Xnumber 0 number lt message gt lt message gt lt error gt lt clean_up gt 1 lt clean_up gt lt info gt first step conf creation lt info gt molecule set in cc cluster in xml molecule set in molecule set out cc cluster out xml molecule set out job schedule lt will be executed according to the step number gt step lt steps will be executed according to the step number gt lt number gt 1 lt number gt lt might be used in the output error messages gt lt info gt conf creation lt info gt lt file of output molecule set not needed for input gt molecule set out stepi out xml lt molecule_set_out gt lt method string of calculation gt lt method gt CF MOPAC CONF GEN lt method gt lt status waiting running ready gt lt status gt waiting lt status gt Step 1 lt error gt lt number gt 0 lt number gt lt message gt lt message gt lt error gt step step lt number gt 2 lt number gt lt just a name used in the output error messages gt lt info gt cluster
10. UCE TO UNIQUECODE The unique codes of the structures of the set are checked against the reference structure Conformers with different uniquename than the reference structure will be neglected Writing PRINT CONF INFO prints listing of molecule names and relative energies on screen not important for calls from GUI WRITE ENERGY FILE writes an energy file for each molecule of the current set The structures and energies will be taken from the molecule set directly The relative to execution directory path used is path name energy with path path defined by subtag see table 1 a name molecule name as defined in molecule name gt The level description printed to the energy files can be given in a subtag see table 1 a The Molecule Set coordi 22 nate file entries will be updated COPY COSMO FILE copies the cosmo files of the relative path to execution di rectory path path name cosmo With path path defined by subtag see table 1 a name molecule name as defined in molecule name defined or a global name name cO n cosmo see subtag in tab 3 if Miscellaneous GET UNIQUECODE gets the 12 character uniquecode COSMOfrag routines fo numbers lt 0 All structures that can be read will be used If the uniquecode calculation fails NONAMEOO00000 will be set instead all molecules of the set The method will ignore errors error r
11. a GmbH amp Co KG Fluid Thermodynamics noutational Chemistr nd Computational Chemistry and I COSMOconfX User Guide Version 3 0 Jul 2013 Copyright by COSMOlogic GmbH amp Co KG Imbacher Weg 46 51379 Leverkusen Germany cosmotherm 9 cosmologic de www cosmologic de 1 MUM CRS EA ws o E E E A bare tentative esate dca edic uq dre T 3 T T IrtFOdUGUODo usn seis od sel ado eno qa Ped See ve aai dna orsi DOR Soc ed aio DU ER UE MURDER 3 Introduction to the COSMOconfX graphical user interface GUI eesssss 6 PEU C II PME 6 2 25 Projects and JODS cos EATUR RH REUS 6 2 3 The Start Set and Results Set panel sss nennen enn 8 2 4 TheJoBDEFINITION panel 5 oriri et eric reuse e ec ve RE Pes eei nEaN i 9 2 5 Running jobs locally or remote ssssessssseseseeereneneenennnnnnnn A nnne nnn 11 2 6 d alcilatio nti etes etc anstatt ue lieu edat vt e E ab dabis 13 2 7 Extracting results dure a iei a Wiad 13 2 8 THE JOD Status sections ien De nnne 14 COSMOconf Linux command line version essen enne 14 3 1 Installation LinUx os ideo coire ea esee ecito teh aote cett ea eder ei sti Cere aa gea cea dada 14 3 2 Howto use the command line version eue rr tette etie rrt a e dee dn en 14 3 3 Directories and file MANICS cs aite ce etos metere bl Gode ty aede buf aa uet ruis 15 3 4 EXAMP lE c circa eei n tol Ee eire HIS EO Ser e ee Tie a E 16
12. and set this template to all jobs of the project Status MoleculeSetOut Error Error message Parameter 4 Run the project Start the job on the local machine Ooa Because we allow for the use of one processor default the first job molecule is running while the others are queued for execution DODE ff Project List 9 f First Project iy aspirin 3 start Set 3 Job Definition o ethanol 3 Start Set 3 Job Definition o glycerol 3 Start Set 3 Job Definition Now we wait until all calculations have been finished the icons should change to f 5 Extract the results Select the project and click the Extract all results button OC c Now chose the result directory me ai S Extract Results to Save In L7 Results BP TZVP COSMO ES allal m v Rename Cx Folder name CACC FilesiResults BP TZVP COSMO Files of Type X Save Cancel In our example we use a directory name that reflects the level of the conformers that have been created Results BP TZVP COSMOY The cosmo files of the conformers can be found in the chosen directory By default the numbering follows the COSMOtherm convention 2 Introduction to the COSMOconfX graphical user interface GUI 2 1 General The COSMOconfX GUI consists of three sections A The project organization section B The job window conta
13. as calculated in an ideal gas i e vacuum and the final results are energy files The COSMO templates will generate conformers relevant for the liquid phase and the final results will be cosmo files If cosmo and energy files are needed we recommend using the combined templates The calculation will be much faster than doing both calculations separately and the u clustering which cannot be used in pure gasphase procedures yields a conformer set especially adjust ed for COSMOtherm calculations Within each group the templates are further divided according to the details of the calcula tion e BP SVP AMI indicates a quick semi empirical AM1 geometry optimization with a BP SVP single point density functional calculation This level is very fast at the cost of some accuracy e BP TZVP indicates a full geometry optimization with density functional theory and a medium sized basis set This is the standard level for COSMOtherm e BP TZVPD FINE indicates a full geometry optimization with density functional theory on BP TZVP level with a consecutive BP def2 TZVPD single point A FINE cavity is used in the COSMO calculations The basis set is significantly larger and includes dif fuse functions This level is required for the COSMOtherm BP TZVPD FINE parameter izations Note The BP TZVP results are automatically generated on the fly during the calculation The results will thus contains two full sets e MF marks the templates that make
14. cO number ing will be used for single conformer compounds An existing but empty global name tag triggers the use of the struc ture set info as global name WRITE ENERGY FILE path defines the relative to the execution dir path of the direc tory the energy files will be written to relative to the COSMOconf execution directory An empty path default creates a Results of job acrnym gt directory job acronymis the name of the job definition xml file global name The energy files will be sorted by energy and renamed global name cx energy x 0 1 n The cO number ing will be used for single conformer compounds An existing but empty global name tag triggers the use of the struc ture set info as global name add comment defines the additional info given in the 2 line of the energy empty file The string ENERGY number will be extended by String the string defined in this tag In order to be consistent with the COSMOtherm conventions this should be METHOD b p BASIS def TZVP for the BP TZVP COSMO database and METHOD b p BASTS def SVP for the BP SVP AM1 database PRINT_CONF_INFO n print optional number of conf to be printed all conf will be printed defaults defined in Job pm fixed balloon options used verbose 1 forcefield MMFF94 mff fullforce nlnitialDimensions 6 keeplnitial nobadmodels randomSeed 42 expand
15. cal mol vnn clust thresh percentage of nuc nuc repulsion deviation 0 05 95 CLUSTER SMS sms threshold Sigma Match Similarity SMS threshold 0 95 ediel weight weight factor that scales the dielectric energy in the cluster 1 0 ing procedure CLUSTER MU mu threshold chemical potential threshold in kcal mol 0 2 kcal mol det lile definition file name file containing the definition of the mix clus tures used for the calc of the chem pot See default file ter mu def for format description REDUCE BY E MAX energy window defines the energy window in kcal mol 20 kcal mol n max maximal number of surviving molecules 50 REDUCE TO UNIQUECODE reference Molecule set XML with one structure The XML files needs to no default be located in the same directory as the input set mole cule set Tr ADD MOLECULE SET File defines the molecule set XML file path relative to execution no default directory This sub tag must be defined COPY COSMO FILE Path defines the relative to the execution dir path of the direc tory the energy files will be written to relative to the COSMOconf execution directory Only the last directory of the path will created automatically An empty path default creates a Results of job acrnym gt directory 25 job acronymis the name of the job definition xml file global name The cosmo files will be sorted by energy and renamed global name cx cosmo x 0 1 n The
16. commend using the CHECK PASSWORD SETTINGS option Set Parameter for external Job Note runs only on Linux Unix systems Select settings test b Data for remote system ServeriiP 10 0 0 777 max total number of CPUs User test user number of CPUs in use j Password Check workload Check Password Settings Configure Work directory home test user COSMOconfX Jobs TURBOMOLE directory software TURBOMOLE COSMOcont directory Isoftware cosmoconf 1 o Check every 1 min C Use queuing system Delete Settings Clear Add New Load Settings Cancel Save Settings OK The paths that need to be adjusted are WORK DIRECTORY Already existing directory that will be used for the COSMOconf calculations Please note that the user needs read and write permissions in this directory TURBOMOLE DIRECTORY Path to the TURBOMOLE installation This path is named STURBODIR in the TURBOMOLE documentation COSMOCONF DIRECTORY Path to COSMOconf installation beside other files this di rectory contains the cosmoconf job wrap pl and the install script On the remote machine the jobs run like local jobs The input data is transferred to the re mote machine and the results are copied back to the local machine Especially for bigger molecules this may take a few seconds the transfer icon will appear Therefore the status of the job see job definition
17. contract pStereoMutation 0 00 26 Example Job definition XML lt xml version 1 0 encoding 1580 8859 1 general remarks error number 0 gt normal termination error number 0 gt error the error message should contain some description of the problem job error Xnumber 0 number lt message gt lt message gt lt error gt lt clean_up gt 1 lt clean_up gt lt info gt first step conf creation lt info gt molecule set in cc cluster in xml molecule set in molecule set out cc cluster out xml molecule set out job schedule lt will be executed according to the step number gt step lt steps will be executed according to the step number gt lt number gt 1 lt number gt lt might be used in the output error messages gt lt info gt conf creation lt info gt lt file of output molecule set not needed for input gt molecule set out stepi out xml lt molecule_set_out gt lt method string of calculation gt lt method gt CF MOPAC CONF GEN lt method gt lt status waiting running ready gt lt status gt waiting lt status gt Step 1 lt error gt lt number gt 0 lt number gt lt message gt lt message gt lt error gt step step lt number gt 2 lt number gt lt just a name used in the output error messages gt lt info gt cluster creation lt info gt lt just a name used in the output e
18. culation for COSMOtherm FINE level TM More information can be found in the corresponding def files Conformer generation CF_MOPAC_CONF_GEN CF MOPAC7 conformer generation BALLOON CONF GEN Balloon will be used for the conformer generation The result molecule set consists of MMFF94 structures and energies 21 Clustering CLUSTER GEODIS geometry clustering using the geodis algorithm CLUSTER EVNN clustering using the energy and the nuclear nuclear repulsion energy CLUSTER SMS clustering using the sigma match similarity COSMO results only CLUSTER MU clustering using COSMO RS chem potentials COSMO re sults only Data sorting reduction amp adding SORT BY E sort by energy ADD MOLECULE SET adds a molecule set XML defined by the file tag see tab 1a to the current molecule set The file must be defined Name conflict have to be avoided by the user The routine checks name conflicts and quits with an error if two molecules share the same name REDUCE BY E MAX reduce data set Use maximal number see definition of molecules with a relative to the min conformer energy within a defined energy window The number of surviving molecules is defined by the tighter criterion max number of molecules or energy window A sort by energy will be done before the reduce algorithm starts Therefore the results can be expected to be sorted RED
19. diedenho COS PAPE olojo linuxto linux4 TM65 diedenho diedenho home auto diede scridiedenho COS Iscridiedenho COS Isoftware TURBOM o PIENE Hint To add new remote systems just submit a job on the remote machine and save the settings just before starting the job OK Cancel 2 6 Calculation time COSMOconf uses quantum chemistry calculations for accurate results Though density func tionally theory is clearly a fast quantum chemistry method the calculation of hundreds of geometry optimization may take quite some time The following table provides a rough guideline on typical calculation times on a standard CPU 2 7 Number of atoms 12 20 40 100 Extracting results Timescale Minutes Hours Days Weeks The result extraction method can be called for e Each job context menu or MANAGE JOB button individually e Awhole project context menu MANAGE JOB button or the extract results icon 4 from the tool bar the results of all jobs of the selected project will be extracted The cosmo energy files will be extracted to the chosen directory By default the COSMOtherm conformer nomenclature will be used RENAME cx activated All molecules 4 Extract results to wem G My_Results 3 Projects Speichern in CC_Files C3 cosmocontProject C3 First Project 7 leu eS cx Biz v Rename Cx Ordnername
20. e Files of Type list For file types that allow for 2D and 3D structures it s important to use the 3D variant 3 2 methoxyethanol xyz L3 aceticacid 2 ethylhexylester xyz l aspirinxyz ethanolxyz alycerol ayz 3 Set the JoB DEFINITION In order to set the same JoB DEFINITION this is the procedure for the conformer search to all molecules Select the project and use the SeT JoB DEFINITION button det COSMOconf File Edit Run Extras Files of Type Molecule cosmo fcos cos ml2 pdb sdf sd mol xyz energy coord chem3d c3d c3d1 c3d2 cc1 ccf car arc ait pie Running Jobs Local 0 2 Remote 0 1 LD start set D Job Definition ethanol C Start set D Job Definition glycerol 3 Start Set L3 Job Definition Used Template Info Number Name Stop No of CPU Machine aspirin Not Started Local Not Started Local D 1 2 ethanol 3 glycerol Not Started Local Start Set Job Definition Result Set Info Number of Molecules 1 Level not defined ID Name Charge Rel Energy kcal mol Type Error message 1 glycerol costo Tempates COSMO Templates IBP SVP AM1 COSMO BD SVD 4 Now choose BP TZVP COSMO
21. efine an input set and a job definition for every job In most cases only one input struc ture e g ethanol is needed and COSMOconf will create a whole set of con DENTON formers C Within a project the same Jos DEFINITION can be easily applied to all jobs or each job can have a different JoB DEFINITION In the same way it is possible to submit all jobs of a project with a single click or to submit each job separately The tool bar on top of the GUI is a collection of actions that are necessary for a typical COSMOconf run All actions in this bar will work simultaneously on the whole project all jobs of the project CREATE NEW PROJECT The path to the project directory has to be chosen If a project name is added to the path a subdirectory with the chosen name will be created E g we chose the CC Files directory and add the project name First Project C ACC_Files First_Project Open a closed project open the cconf project file fj Save selected project e Create a new job in the actual project Molecular 3D structure files can be picked with a file chooser menu Each selected structure will create a new job in the se lected project The name of the structure file will be automatically used as job name This name can be changed within the right mouse button menu Rename this calculation Set job definition to the current project All jobs of the project receive the same job definition exce
22. in the ERROR MESSAGE column For start sets the molecular charge can be set in the CHARGE select box The charge can also be set in the charge column of every single structure of the set Start Set Job Definition Result Set Info Number of Molecules 1 Level not defined Charge Manage Molecules o Add Molecule s Build Molecule s ID Name Charge Rel Energy kcal mol Type Error Error message 1 butyltrimethylammonium C3 cosmo A context menu right mouse button or the MANAGE MOLECULES button can be used to apply several options to one or several selected structures Depending on the type of set Start or Result the option may vary SHOW MOLECULE The structures of the actual selection will be displayed in a mole cule viewer CREATE NEW CALCULATION The selected structures will be used as Start Set for a new job The job will be named after the first structure of the selection This option works for all sets and can be used for subsequent treatment DELETE Delete the selected structure Only for jobs that have not been started yet EDIT MOLECULE Start a structure editor to modify the current structure Only for jobs that have not been started yet The Fe samotecue button of the Start SET panel is similar to the Loan MOLECULE button of the tool bar The important difference is that it adds molecules to the current START SET instead of creating a new job This option can be usef
23. ins the Jos DEFINITION the START SET and one or more RESULT SETS C The job status section somos 0 cc c mE c a File Edit Run Extras Help he 8 O6 8 RunningJobs Local 072 Remote 0 Memory COSMOcont BSATEN Name No of CPU Machine P ft ProeatList 2 methoxyethanol Not Started 1 ea MyProject Jaceticacid 2 ethylhexylester Not Started w glycerol Not Started 3 Start Set 1 Job Definition a aceticacid 2 ethylhexylester g 2 methoxyethanol 3 Start Set C Job Definition Info Vg glycerol rr J jen T Number of Molecules 1 Level not defined B Charge Manage Molecules e Add Molecule s Start Set 3 Job Definition Build Molecule s g A Name Charge Rel Energy kcal mol Error message Start Set Job Definition Result Set 2 methoxyethanol z Manage Job 2 2 Projects and jobs The project organization section holds the list of projects and their jobs Each project might consist of one or more jobs of different types In a standard COSMOconf calculation each job represents one molecules of interest A job can consist of one or more molecules START SET and a JoB DEFINITION The JOB DEFINITION provides the information about the consecutive steps which will finally convert the input molecule s to the RESULT SET Therefore the user needs to d
24. ithout xml join extraction to the general result directory chosen by the user directory subdirectory of the general result directory that should be used if extractable separate is used Method the implemented methods are listed in table 1 The acro nym from table 1 has be used here Status This tag provides the work flow status information Allowed values are waiting running ready off l n a new input all status values should be set to waitingoroff A missing status will be interpreted as waiting Error job step error description number lt 0 gt error The error description can be found in the message tag Undefined error numbers will be interpreted as O 29 Table 3 Special job requirements Job Type Acronym Special structure XML requirements QM calculation AM1 GAS AM1 COSMO BP TZVP COSMO BP TZVP GAS BP SVP COSMO SP BP SVP GAS SP CF_MOPAC_CONF_GEN only one structure BALLOON_CONF_GEN only one structure Clustering CLUSTER_GEODIS energy of molecule must be defined CLUSTER_EVNN energy of molecule must be defined CLUSTER_SMS only cosmo files defined by the coordinate file and name tag see table 1 All cosmo cos files must be located in the same directory CLUSTER_MU only cosmo files defined by the coordinate file and name tag see table 1 All cosmo cos files must be located in
25. mental understanding on conformer gen eration is recommended The default templates are constructed to yield good results for the majority of tasks i e for organic compounds of small to medium size 1 to 60 Atoms COSMOconf will work fine for larger molecules but a user defined workflow might provide some benefits either in calcula tion time or quality Some of the presented features can be accessed via the graphical user interface other are only available from the command line 17 4 1 The COSMOconf workflow The COSMOconf workflow consists of unit operations steps working on sets of structures The In Out sets for these steps are lists of molecules conformers in XML format The results of the n step will be used as input for the n 1 step Optionally intermediate molecule sets can be saved this option currently not available from the GUI A typical workflow and all default templates for JoB DEFINITIONS will start with only a single structure and conduct the following basic steps 1 Conformer generation which can be either done by COSMOfrag and MOPAC or by Balloon This step generates as many different structures as possible 2 Checkand Reduction Throw out identical conformers higher energy conformers conformers with wrong stereochemistry and so on There are multiple possibilities to select for those conformations needed 3 Quantum Chemistry calculations A single point or geometry optimization to provide inf
26. network Number Method Info Status MoleculeSetOut Error Error message Parameter 1 BALLOON_CONF_GEN conf creation using b waiting o View Set Parameter 2 REDUCE TO UNIQUECODE consistency check us waiting 0 View Set Parameter 3 SORT BY E sort w rt energy waiting 0 4 CLUSTER_GEODIS geodis clustering thr waiting of View Set Parameter 5 REDUCE_BY_E_MAX reduce to 150 structur waiting 0 View Set Parameter 6 BP SV P COSMO SP BP SV P cosmo singl waiting 0 7 CLUSTER_MU clustering w r t chem waiting 0 View Set Parameter 8 REDUCE BY E MAX reduce to 50 structure waiting 0 View Set Parameter 9 BP SV P COSMO LOOSE BP SV P opt with loo waiting E of 10 SORT_BY_E sort w r t energy waiting 0 11 CLUSTER_GEODIS standard geodis clust waiting 0 View Set Parameter 12 CLUSTER_MU clustering w r t chem waiting o View Set Parameter 13 REDUCE_BY_E_MAX reduce to 10 0 kcal m waiting 0 View Set Parameter 14 BP TZVP COSMO BP TZVP COSMO opti waiting 0 15 SORT BYE _ sort w r t energy waiting 0 IE 16 CLUSTER GEODIS standard geodis clust waiting 0 View Set Parameter 17 I CLUSTER MU clustering w r t chem waiting 0 View Set Parameter 18 REDUCE BY E MAX reduce to 10 conform waiting 0 View Set Parameter an annt enin marca I uM al Naranai Default Templates The default templates are divided into three groups gasphase templates COSMO templates and gasphase COSMO templates The gasphase templates will produce conformations
27. onf pl without arguments lt input dir Complete path of input file directory List of allowed input file types car Accelrys MSI Biosym Insight Il CAR format cosmo COSMOlogic COSMO file arc MOPAC cartesian arc file ml2 Sybyl Mol2 format mol2 Sybyl Mol2 format pdb Unimolecular protein data bank format file XYZ XYZ cartesian coordinates format energy COSMOlogic energy file sdf MDL Isis unimolecular 3D SDF V2000 3 3 Directories and file names A calculation creates the following directories CMcal This directory holds the subdirectories of the molecules which contain all MOPAC COSMOfrag and TURBOMOLE calculations Results of job These directories hold the final cosmo and energy files respectively The different con formers are numbered cO cn accordingly to the COSMO data base convention The con formers are ordered with respect to increasing energy The file glucose cO cosmo for in stance corresponds to the energetically DFT energies favorable conformer Please note the gas phase energies energy files have similar names but the order corresponds to the MOPAG7 is the public domain version of MOPAC A GENERAL MOLECULAR ORBITAL PACKAGE ORIGINAL VERSION WRITTEN IN 1983 BY JAMES J P STEWART AT THE UNIVERSITY OF TEXAS AT AUSTIN AUSTIN TEXAS MODIFIED TO DO ESP CALCULATIONS BY BRENT H BESLER AND K M MERZ JR 1989 locally modified by Andreas Klamt COSMOlogic For more details about MOPAC7
28. ormation for better reduction or clustering 4 Clustering To select only those conformations that show a different physical behav ior the SMS or u clustering routines can be used The steps 2 to 4 are usually repeated several times with different settings to finally produce a small set of relevant conformers Apart from the above typical approach the user can define anything he needs One possible example would be to use a whole set of conformations as a starting point leave out the con 2 http users abo fi mivainio balloon Mikko J Vainio and Mark S Johnson 2007 Generating Con former Ensembles Using a Multiobjective Genetic Algorithm Journal of Chemical Information and Modeling 47 2462 2474 18 former generation with COSMOfrag or Balloon and just do some reduction or clustering or qauntum chemistry 4 2 Unitoperations steps The necessary information has been contracted in several tables Table 1 Lists the allowed steps These are methods tags inside a step Table 1a Lists the allowed options and parameters for all steps of table 1 Table2 General tags used outside steps for clean up or results extraction Tbale 3 Limitations of certain methods e g conformer generator will work only on one structure Some steps allow for the definition of calculation type specific parameters These options can be given in an extra tag subtag of step Example How to use parameter tags step lt METHOD gt PUT THE METHO
29. panel cannot be updated like for local calculations The GUI does check the remote jobs at regular intervals which can be defined by CHECK EVERY param eter The maximum number of CPUs on the remote i e the number of processes the GUI is allowed to send to the remote machine is defined by NUMBER OF CPUs For JOB S The NUMBER OF NODES parallel TURBOMOLE parameter determines the number of nodes that should be used for the parallel run of TURBOMOLE for each job Because each parallel execution gen erates communication overhead we recommend running several serial jobs at the same time instead using the same amount of nodes for one parallel job Please note the FINE level COSMO calculations have not been parallelized yet All job definitions containing the FINE level will be started as serial jobs automatically The current workload of the remote machine can be checked with the CHECK WORKLOAD op tion The CONFIGURE button opens an overview of all defined remote machines The TOTAL 13 AVAIL CPUS can be used to ensure that the Use max 4 CPU value does not exceed the physical limits of the machine This check is switched off 1 by default Remote machines can be deleted via the context menu l P Server lP User Work directory TURBOHOLE direct total avail RAM MB Use max CPU total avail CPUs linux4 test diedenho diedenho scridiedenho COS home auto diede isoftware TURBOM iscri
30. pos es RENAME THIS JOB Change the name of the job The name of the structure in the Input Results Sets will not be changed but the new name will be used in the result extraction the extracted files will be named after the job CLOSE The job will disappear from the list but the data will be kept on disk It can be re opened later DELETE All data will be deleted REMOVE JOB FROM QUEUE A queued job can be removed from the queue STOP THIS JOB The selected job will be stopped It can be continued later EXTRACT RESULTS The results of the selected jobs will be extracted to the user defined directory see the Extract results paragraph below SAVE AND RUN THIS JOB The current settings will be saved and the job will be started or queued see the How to start a job paragraph below The following icons indicate the job status Job terminated properly Erroneous job execution See error message in Job Definition and or Molecule Set amp 4 Job before execution Job is running Job in queue waiting for a free processor The job has been stopped by the user tt OQ fi Data transfer from remote to local machine 2 3 The Start Set and Results Set panel The table can be sorted with respect to the REL ENERGY relative energy by clicking on the column headline Errors that occurred during the calculations are indicated by a negative number in the ERROR column and some information about the problem can be found
31. pt the ones that have been defined before G Save and run the project on the local computer Save and run the project on the external computer via network Extract all result files of the current project A Project List Eg Mpa ma Close 4 Delete Set Job Definition a 0 Extract Results G3 51 open Job An m te Add Job U c amp 4 a Add empty Job r amp Save Project LL OPEN JOB ADD EMPTY JOB The context menu right mouse button or MANAGE PROJECT button can be used to close or delete the whole project Use Close if you like to be able to open the project again The DELETE option will delete all data on the disk i e the project cconf file and the data of all corre sponding jobs In addition the FiLE menu offers the following options To open a previously closed job choose the jobdefinition xml file of the job Allows for the creation of an empty job with now molecules inside The molecules can be added with the Add and Build buttons of section B later on In the typical COSMOconf usage generation of a conformer set from one start structure each molecule will be represented by a job A job can be modified using the job context menu right mouse button or the MANAGE JOB button The available options depend on the status of the job ViEW JOB DIRECTORY Open the job directory the directory of the job execution in a browser window This option is mainly used for debug pur
32. rror messages gt lt file of output molecule set not needed for input gt molecule set_out gt step2 out xml molecule set out lt method string of calculation gt lt method gt CLUSTER GEODIS lt method gt lt status waiting running ready gt lt status gt waiting lt status gt lt error gt number 0 number message message lt error gt step job schedule lt job gt Step 2 27 Table 2 Tag description of job XML Error Tag Description global error description number 0 gt error The error description can be found in the message tag The error on the job level contains general errors which cannot be re lated to the steps defined If a specific step error occurs the job error will be set to a negative value too gt the error definitions of the job step should be checked if the job error number lt 0 An undefined error number will be interpreted as O Info optional info string clean up reasonable clean up 1 on O off calc directories op tional default 1 mo ecul e set in input XML see molecule set XML In OUT set The rela tive path to execution directory needs to be given mo ecul e set out attribute extractable attribute directory output XML see molecule set XML In OUT Set The rela tive path to execution directory needs to be given The extrac
33. sure correct read write and execute setting the installation should be done by a member of the user group that will use the script later on 1 Unpack the COSMOconf archive into a chosen directory gunzip COSMOconf tar gz tar xvf COSMOconf tar 2 Copy the license file 1icense ctd to the installation directory the directory that has been chosen in step 1 3 Change into the installation directory and start the COSMOconf installation script and follow the instructions install If the command line COSMOconf version should be used it might be convenient to include the COSMOconf directory the one where you executed install in the PATH We recommend to define the new PATH in the local environment of the user bashrc cshrc etc For a bash user the entry looks like export PATH path to COSMOconf S PATH 3 2 Howto use the command line version In order to do a series of calculations one needs to provide a directory with 3D input struc tures The script needs a list of the structure input files e g water Xxyz methanol xyz H30 xyz 1 15 The molecular charge has to be given for charged molecules The script can be started as follows COSMOconf pl 1 input list m method din input dir gt gt lt logfile gt Parameters in brackets are optional method Describes the quantum mechanical level A brief description can be found in the cosmoconf p1 help message simply execute cosmoc
34. table and directory attributes define the re sult extraction of the COSMOconf GUI extractable no no extraction of the set separate extraction to the subdirectory defined by the directory attribute If the directory attribute is missing the subdirectory will be named like is the name of the set without xml join extraction to the general result directory chosen by the user directory subdirectory of the general result directory that should be used if extractable separate is used job schedule set of job steps Step definition of a job step Subtags of job schedule Number The steps of the jobs will be executed according to their number E g a step 99 will be executed before step 1 regardless of the order in the XML document 28 Info molecule set out attribute extractable attribute directory just some info that will be printed to the output optional If defined the output structure set of this particular set will be written to the given file name format molecule set XML format the relative path to execution directory needs to be given optional The extractable and directory attribute define the result extraction of the COSMOconf GUI extractable no no extraction of the set Separate extraction to the subdirectory defined by the directory attribute If the directory attribute is missing the subdirectory will be named like is the name of the set w
35. the same directory
36. ul in a step by step procedure e g if one likes to perform a QM calculation on a set of input structures To add more than one structure however is not useful for the standard conformer generation because the current conformer generators are designed for one input structure only 2 4 The Jos DEFINITION panel Each job needs a job definition i e a list of methods that should be applied successively Because the job definition holds information about the status of the execution it cannot be set or changed for running or terminated jobs The job definition can be set for each job in dividually context menu of the job or MANAGE JOB button or for the whole project depend ing on whether the project or the job is selected 10 The status of jobs running on the local machine will be updated frequently Remote jobs sta tus information will not be updated during the calculation The results will be copied at the end of the calculation and therefore the status will be updated only once at the end The number of molecules nmolz at the end of the step can be found in the status column Start Set Job Definition Result Set Gasphase Templates ml BP TZVP COSMO Y Gasphase COSMO Templates v User Templates mi Used Template Info BP TZvP COSMO Add Step A iv Save as Template gt Run This Job local Run This Job
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