From: Kasam, Vinod (vkasam_at_coh.org)
Date: Thu Sep 13 2012 - 10:52:31 CDT
Dear NAMD users,
I am running a minimizationin NAMD using the parameters shown below. When I ran minimization using the same parameters in two different folders with the same input (protein), I am ending up in different results.
The co-ordinates of the proteins and the energy values after minimization are different. However, if I do not use GBIS (comment out GBIS input parameters), the results are same and just FINE.
I am new to NAMD and I am using NAMD2.8 version, can some explain me why are the results different for the same input if I use GBIS.
Thank you,
Vinod
# MOLECULAR SYSTEM
structure min_WT-chain_D.psf
coordinates min_WT-chain_D.pdb
# FORCE FIELD
paraTypeCharmm on
parameters par_all22_prot_cmap.inp
# APPROXIMATIONS
switching on
switchdist 15
cutoff 16
pairlistdist 17.5
#margin 3
exclude scaled1-4
1-4scaling 1.0
dielectric 3
seed 20111012
#INTEGRATOR
timestep 1.0
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#GBIS - Implicit solvent
GBIS on
solventDielectric 78.5
ionConcentration 0.2
alphaCutoff 15
# PERIODIC BOUNDARY CONDITIONS
cellBasisVector1 51.76400065422058 0 0
cellBasisVector2 0 45.07099914550781 0
cellBasisVector3 0 0 43.320000648498535
cellOrigin 28.250900268554688 39.77300262451172 7.405788421630859
# WRAPPING
wrapAll on
# OUTPUT
outputname monomerA-crystal-min
dcdfreq 500
xstfreq 10000
outputenergies 10
outputtiming 100
binaryoutput no
binaryrestart yes
# RESTART FILES
restartname res
restartfreq 1000
restartsave yes
# TEMPERATURE CONTROL
temperature 0
minimize 1000
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