# initial config
# this is your standard pdb file (generated using PSFgen) that you put under common folder
coordinates ../common/1vii0RMSD.pdb
temperature 0

# output params
outputname osman
binaryoutput no

# integrator params # 2 fs step size
timestep 2.0

# force field params
# these should be the same as the lines you have used during your first NAMD run
# that you generated the .dcd file
paraTypeCharmm on
structure ../common/1vii0RMSD.psf
parameters ../common/par_all27_prot_lipid.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 13.5
stepspercycle 10

# provide information about the cell size
# these are yet again same as that of your previous .conf file
cellBasisVector1 42. 0. 0.
cellBasisVector2 0. 35. 0.
cellBasisVector3 0. 0. 35.
cellOrigin 4. 1.5 2.5
wrapAll on

# Atoms in group 1 have a 1 in the B column; group 2 has a 2. This script will calculate their interaction forces
pairInteraction on
pairInteractionFile ../common/pair.pdb # this is the file where you provide the group numbers
pairInteractionCol B # we use the B-Factor column to specify which atoms belong to group 1 & 2
pairInteractionGroup1 1 # flag to include atoms in group 1
pairInteractionGroup2 2 # flag to include atoms in group 2

# First frame saved was frame 0.
# You can check which frame numbers are written in your .dcd file
# by looking at the first column of your .xst file
set ts 0

# this line opens the .dcd file for reading and deriving energies
coorfile open dcd 1vii0RMSD.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
# this is your incremental time step
incr ts 20000
}
coorfile close