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Moduli koji dopremaju CHARMM u vašu okolinu definirani su u tablici niže:
Verzija | Modul |
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47b1 | charmm/47b1 |
Primjer korištenja
Primjer serijskog korištenja
Code Block | ||||
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#!/bin/bash #$ -N charmm #$ -cwd module load charmm/47b1 charmm < input.inp > output.out |
Primjer paralelnog korištenja
Code Block | ||||
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#!/bin/bash #$ -N charmm #$ -cwd #$ -pe *mpi 4 module load charmm/47b1 mpirun -np ${NSLOTS} charmm -i input.inp -o output.out |
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Korištena input datoteka
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* CHARMM input script to run an MD simulation on a * system of 32 water molecules BOMLEV -3 READ RTF CARD * This is the water residue * 47 1 MASS 1 H 1.0 ! Water - Hydrogen Atom MASS 2 O 16.0 ! Water - Oxygen Atom RESIDUE H2O 0.0 ! Water Model and its charge ATOM OH2 O -0.82 ! Oxygen atom and charge ATOM H1 H 0.41 ! Hydrogen atom and charge ATOM H2 H 0.41 ! Hydrogen atom and charge BOND OH2 H1 OH2 H2 ! Define atom-atom connections THETA H1 OH2 H2 ! Define dihedral angle PATCH FIRST NONE LAST NONE ! Do not patch the termini END ! =================================================================== READ PARAMETERS CARD * Bond and angle constraints for water * BOND H O 450.0 0.9572 ! Force constant of the H-O bond THETA H O H 55.0 104.52 ! Equilibrium angle in degrees NONBONDED O 0.0 -0.1521 1.7682 ! Well-depth and van der Waals radius H 0.0 -0.04598 0.2245 ! Well-depth and van der Waals radium END ! =================================================================== READ SEQUENCE H2O 32 GENERATE WAT SETUP READ COORDINATES CARD FREE * Oxygen Coordinates * 32 1 1 H2O OH2 -4.5 -4.5 -4.5 1 2 H2O OH2 -1.5 -4.5 -4.5 1 3 H2O OH2 -4.5 -1.5 -4.5 1 4 H2O OH2 -4.5 -4.5 -1.5 1 5 H2O OH2 -1.5 -1.5 -4.5 1 6 H2O OH2 -1.5 -4.5 -1.5 1 7 H2O OH2 -4.5 -1.5 -1.5 1 8 H2O OH2 -1.5 -1.5 -1.5 1 9 H2O OH2 -4.5 -4.5 1.5 1 10 H2O OH2 -1.5 -4.5 1.5 1 11 H2O OH2 -4.5 -1.5 1.5 1 12 H2O OH2 -4.5 -4.5 4.5 1 13 H2O OH2 -1.5 -1.5 1.5 1 14 H2O OH2 -1.5 -4.5 4.5 1 15 H2O OH2 -4.5 -1.5 4.5 1 16 H2O OH2 -1.5 -1.5 4.5 1 17 H2O OH2 -4.5 1.5 -4.5 1 18 H2O OH2 -1.5 1.5 -4.5 1 19 H2O OH2 -4.5 4.5 -4.5 1 20 H2O OH2 -4.5 1.5 -1.5 1 21 H2O OH2 -1.5 4.5 -4.5 1 22 H2O OH2 -1.5 1.5 -1.5 1 23 H2O OH2 -4.5 4.5 -1.5 1 24 H2O OH2 -1.5 4.5 -1.5 1 25 H2O OH2 -4.5 1.5 1.5 1 26 H2O OH2 -1.5 1.5 1.5 1 27 H2O OH2 -4.5 4.5 1.5 1 28 H2O OH2 -4.5 1.5 4.5 1 29 H2O OH2 -1.5 4.5 1.5 1 30 H2O OH2 -1.5 1.5 4.5 1 31 H2O OH2 -4.5 4.5 4.5 1 32 H2O OH2 -1.5 4.5 4.5 ! format above is (segment #) (residue #) (residue name) (atom type) ! (x coor) (y coor) (z coor) HBUILD PRINT COORDINATES ! The psf file contains all the information on the makeup of the system OPEN UNIT 1 WRITE CARD NAME water.psf WRITE PSF CARD UNIT 1 * PSF for 32 water molecule system * ! The CRD file will contain the coordinates of all the atoms in the system ! written in CHARMM format OPEN UNIT 1 WRITE CARD NAME water.crd WRITE COORDINATE CARD UNIT 1 * Initial coordinates for starting point of simulation * ! The PDB file will contain the coordinates of all the atoms in the system ! written in Protein Data Bank format OPEN UNIT 1 WRITE CARD NAME water.pdb WRITE COORDINATES PDB UNIT 1 * Initial coordinates for starting point of simulation * CRYSTAL DEFINE CUBIC 13.0 13.0 13.0 90.0 90.0 90.0 CRYSTAL BUILD NOPERATIONS 0 OPEN UNIT 1 WRITE CARD NAME cubic.cry WRITE CRYSTAL CARD UNIT 1 * PBC for simple cubic geometry * SHAKE BONH PARAMETERS SELECT ALL END ! Constrain all bonds to H atoms ! to their parameter values OPEN UNIT 11 WRITE FILE NAME water.dcd DYNAMICS STRT - NSTEP 20000 TIMESTEP 0.001 - NPRINT 100 IPRFRQ 1000 NTRFRQ 5000 - NSAVC 100 IUNCRD 11 IUNWRI 1 - FIRSTT 100.0 FINALT 300.0 TEMINC 50.0 IHTFRQ 500 - IASORS 1 IASVEL 1 ISCVEL 0 IEQFRQ 1000 ICHECW 0 - TWINDH 10.0 TWINDL -10.0 - INBFRQ 25 IMGFRQ 25 CUTNB 12.0 CUTIM 12.0 CTOFNB 10.0 - CTONNB 8.0 SHIFT VSWITCH |
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Slika 1
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Posljednja struktura sustava koji sadrži 32 molekule vode
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nastala dinamičkom evolucijom u vremenu.