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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