vacuum minimisation-reg

From: Revthi Sanker (
Date: Wed Jul 24 2013 - 02:37:12 CDT

Dear all,
I am a novice to performing simulations and NAMD. I intend to perform a
vacuum minimization before solvating the protein. this is the script that
I am using for this purpose. I was informed that we should restrain the the
backbone atoms for this step. If so, how would I do that and how do I
remove the restraints before proceeding to solvation? I would be grateful
for help me in this regard.

paraTypeCharmm on
minimization on

numsteps 2000
structure ptn_psf.psf
parameters modified_par_all36_prot.prm
parameters par_all36_lipid.prm
coordinates ptn_psf.pdb
exclude scaled1-4
1-4scaling 1.0

temperature 0
seed 1234

binaryoutput yes
outputEnergies 1
outputname ptn_gas_min

switching on
switchdist 8.5
cutoff 10
pairlistdist 12

#periodic boundary conditions
cellBasisVector1 144 0 0
cellBasisVector2 0 144 0
cellBasisVector3 0 0 144

PME on
PMEGridSizeX 144
PMEGridSizeY 144
PMEGridSizeZ 144

IMDon no
IMDport 2030
IMDFreq 1

# position-restrained
fixedAtoms on
fixedAtomsFile fixed_atoms.pdb
fixedAtomsCol B # 1.0 in this col.
fixedAtomsForces on

dcdfreq 250
xstFreq 250

thanks in advance :)

M.S. Research Scholar
Indian Institute Of Technology, Madras

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