Unable to reproduce same results in minimization with GBIS

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,

structure min_WT-chain_D.psf
coordinates min_WT-chain_D.pdb

paraTypeCharmm on
parameters par_all22_prot_cmap.inp

switching on
switchdist 15
cutoff 16
pairlistdist 17.5
#margin 3
exclude scaled1-4
1-4scaling 1.0
dielectric 3
seed 20111012

timestep 1.0
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

#GBIS - Implicit solvent
solventDielectric 78.5
ionConcentration 0.2
 alphaCutoff 15

cellBasisVector1 51.76400065422058 0 0
cellBasisVector2 0 45.07099914550781 0
cellBasisVector3 0 0 43.320000648498535
cellOrigin 28.250900268554688 39.77300262451172 7.405788421630859

wrapAll on

outputname monomerA-crystal-min
dcdfreq 500
xstfreq 10000

outputenergies 10
outputtiming 100
binaryoutput no
binaryrestart yes

restartname res
restartfreq 1000
restartsave yes

temperature 0

minimize 1000

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