NAMD minimisation

From: Hua Wong (wong_at_ebgm.jussieu.fr)
Date: Thu Nov 27 2003 - 07:29:27 CST

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Hello. I have trouble with setting up a minimisation under NAMD.
Here is the NAMD script I use....

# NAMD configuration file for PROT

# molecular system
structure PROT.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

#integrator
numsteps 10000
timestep 1

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

# molecular system
coordinates PROT.pdb

#output
outputname PROT_out
#dcdfreq 1000

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

#protocol
temperature 400
langevin no

rescaleFreq 50
rescaleTemp 400

#script

#minimize 400

run 20000

and the results I obtain

ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG

ENERGY: 0 2685892.8098 -99999999.9999 -99999999.9999
-99999999.9999 -13233.6249 99999999.9999 0.0000
0.0000 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999

ENERGY: 1 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999 -99999999.9999 0.0000
0.0000 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999

ENERGY: 2 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999 -99999999.9999 0.0000
0.0000 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999

I am a bit puzzled because someone else made a script that is identical
and it seems to work.....

Any hint?

Thanks

Wong Hua

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