minimization scripts

From: Gerald Quon (
Date: Mon Feb 09 2004 - 12:09:29 CST


I'm a new user and am interested in using NAMD for minimization purposes.
I've downloaded the CHARMM potentials, and tried the following
minimization script, but it does not
seem to minimize my structures very well (when minimizing test native
PDB files, I get structures that are 5-6 angstroms off).

I was wondering if anyone could provide me with a 'standard' minimization
script that I could start off with, or give me suggestions on how to
improve mine? Thanks!

- Gerald Quon
University of Waterloo
Waterloo, Ontario, Canada


# NAMD configuration file for PROT
# molecular system
structure 0.psf

# force field
paratypecharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0

# approximations
switching on
switchdist 8
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20

numsteps 10000
timestep 1

outputenergies 1
outputtiming 100
binaryoutput no
imdon yes
imdfreq 1
imdport 3111

# molecular system
coordinates 0.pdb

outputname 0_out
#dcdfreq 1000

# constraints/Fixed
fixedAtoms on
fixedAtomsFile 0.pdb
fixedAtomsCol B

temperature 400
langevin no

rescaleFreq 50
rescaleTemp 400


minimize 400

run 20000

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