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CHARMM Element Doc/Gamess.Doc 1.1 # File: Gamess, Node: Top, Up: (Chmdoc/Commands.Doc), Next: Description CHARMM Element doc/gamess.doc 1.1 # File: Gamess, Node: Top, Up: (chmdoc/commands.doc), Next: Description Combined Quantum Mechanical and Molecular Mechanics Method Based on GAMESS in CHARMM by Milan Hodoscek ([email protected],[email protected]) Ab initio program GAMESS (General Atomic and Molecular Electronic Structure System) is connected to CHARMM program in a QM/MM method. This method is extension of the QUANTUM code which is described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990). * Menu: * Description:: Description of the gamess commands. * Using:: How to run GAMESS in CHARMM. * Installation:: How to install GAMESS in CHARMM environment. * Status:: Status of the interface code. * Functionality:: Functionality of the interface code. # File: Gamess, Node: Description, Up: Top, Next: Usage, Previous: Top The GAMESS QM potential is initialized with the GAMEss command. [SYNTAX GAMEss] GAMEss [REMOve] [EXGRoup] [QINPut] [BLURred] [NOGUess] (atom selection) REMOve: Classical energies within QM atoms are removed. EXGRoup: QM/MM Electrostatics for link host groups removed. QINPut: Charges are taken from PSF for the QM atoms. Charges may be non integer numbers. Use this with the REMOve! NOGUess: Obtains initial orbital guess from previous calculation. Default is to recalculate initial orbitals each time. BLURred: MM charges are scaled by a gaussian function (equivalent to ECP) Width of the gaussian function is specified in WMAIN array (usually by SCALar command) The value for charge is taken from PSF. Some values of WMAIN have special meaning: WMAIN.GT.999.0 ignore this atom from the QM/MM interaction WMAIN.EQ. 0.0 treat this atom as point charge in the QM/MM potential The atoms in selection will be treated as QM atoms. Link atom may be added between an QM and MM atoms with the following command: ADDLinkatom link-atom-name QM-atom-spec MM-atom-spec link-atom-name ::= a four character descriptor starting with QQ. atom-spec::= {residue-number atom-name} { segid resid atom-name } { BYNUm atom-number } When using link atoms to break a bond between QM and MM regions bond and angle parameters have to be added to parameter file or better use READ PARAm APPEnd command. Also note that QQH type has to be added in the RTF file (see test/c25test/gmstst.inp). If define is used for selection of QM region put it after all ADDLink commands so the numbers of atoms in the selections are not changed. Link atoms are always selected as QM atoms. ======================================================================= # File: Gamess, Node: Usage, Up: Top, Next: Installation , Previous: Description In order to run GAMESS and CHARMM on parallel machines I/O of GAMESS and CHARMM was separated. This is now true even for scalar runs. CHARMM input scripts are the same as before except the addition of ENVIronment commands and GAMEss command itself. GAMESS commands are in a separate file which is pointed to by INPUT environment variable. Names of the files for GAMESS are specefied with environment variables as follows: use ENVIronment command inside CHARMM envi INPUT "test.gms" ! quotes needed for lowercase names envi OUTPUT "test.out" envi PUNCH "scratch/test.dat" envi DICTNRY "scratch/test.F10" envi WORK15 "scratch/test.F15" envi DASORT "scratch/test.F20" or use (t)csh setenv INPUT test.gms setenv OUTPUT test.out setenv PUNCH scratch/test.dat setenv DICTNRY scratch/test.F10 setenv WORK15 scratch/test.F15 setenv DASORT scratch/test.F20 or ksh,sh,bash export INPUT = test.gms export OUTPUT = test.out export PUNCH = scratch/test.dat export DICTNRY = scratch/test.F10 export WORK15 = scratch/test.F15 export DASORT = scratch/test.F20 For complete information about GAMESS input see INPUT.DOC file in GAMESS distribution. (NIH: ~milan/gamess/hp/INPUT.DOC) Example: -------- GAMESS commands have to be in a separate file. Example for the GAMESS input follows:.
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