# initial config
coordinates         RO.pdb
temperature         300

# output params
outputname          ads
extendedSystem      RO_Pro.restart.xsc
binaryoutput        no

# integrator params
timestep            1.0

# force field params

structure          RO.psf
paraTypeCharmm       on
parameters         GO_Water_Na_Cl_Mg_Al_SO4_Acetic_acid.prm
parameters         Lyso.inp
vdwGeometricSigma    yes
exclude            scaled1-4
1-4scaling         0.5
switching          on
switchdist         10.0
cutoff             12.0
pairlistdist       14.0
stepspercycle      20

#particle mesh ewald
PME                  on
PMEGridSpacing       1.0
#PMEGridSizeX         180
#PMEGridSizeY         120
#PMEGridSizeZ         450


# Atoms in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction      on
pairInteractionFile  adsorb.pdb
pairInteractionCol    B
pairInteractionGroup1 1
pairInteractionGroup2 2

# First frame saved was frame 1000.
set ts 0
coorfile open dcd ROI.dcd

# Read all frames until nonzero is returned.
while { ![coorfile read] } {

# Set firstTimestep so our energy output has the correct TS.

firstTimestep $ts
# Compute energies and forces, but don’t try to move the atoms.

run 0
incr ts 1
}
coorfile close