From: Navratna Vajpai (navratna.vajpai_at_unibas.ch)
Date: Sun Jul 31 2005 - 02:24:39 CDT
> Dear Mr/Ms
> Hello.
> I have been doing MD simulations of a peptide for the last couple of
> weeks. I have been using NAMD software( MacOsX version) for these
> simulations. But for some reason or so the MD simulation crash out
> sometimes with an error message and sometimes without. To check for
> the viability of our input files I tried running it on different
> machines, all the other factors remained identical. (including the
> seed number in the files)
> I observed differences in the energies after 50 steps in the output
> file of the two different machines. to my understanding it could be
> related with the computer clock time and so on the two different
> machines it could go little differently. But after some 1ns trajectory
> or so the results look quite different. then I checked the same
> program on the same machine with the same conditions. But to my
> surprise, again I found the difference in the energies in the two
> different runs, although less severe when compared to other case.
> whether this will happen always or there is something wrong with the
> input files. can any body suggest what is happening wrong there. I am
> attaching my input file as well.
> Secondly I would also like to ask you, when I have to restart a MD
> run, whether I have to restart exactly from the same point or have to
> restart with respect to the last restart frequency.
> Thanks for any kind of the help.
> Best regards
> Nav
# NAMD configuration file for peptide
#
set ss /nmr_apps_DarwinPPC/CHARMM/c31b1/toppar
#
set start "yes"
#
set input0 ./TRPpepScp
set input ./output/TRPpep300.restart
set output ./output/TRPpep300
#
set temp 300.0
#
structure ./TRPpepScp.psf
if {$start == "yes"} {
temperature $temp
coordinates $input0.pdb
} else {
coordinates $input0.pdb
binCoordinates $input.coor
binVelocities $input.vel
extendedSystem $input.xsc
}
#******* molecular system
if {$start == "yes"} {
cellBasisVector1 49.0 0.0 0.0
cellBasisVector2 0.0 33.0 0.0
cellBasisVector3 0.0 0.0 33.0
cellOrigin 0.0 0.0 0.0
}
wrapWater on
PME on
PMEGridSizeX 28
PMEGridSizeY 28
PMEGridSizeZ 28
#******* force field
paratypecharmm on
parameters $ss/par_all22_prot.inp
#parameters $ss/par_all22_prot_lipid.xplor
exclude scaled1-4
1-4scaling 1.0
#******* approximations
switching on
switchdist 12
cutoff 14
pairlistdist 16
margin 0
stepspercycle 10
#******* protocol
#seed 74269
seed 26974
#tCouple on
#tCoupleTemp 300
#reassignFreq 40
#reassignTemp 300
##reassignIncr 25
##reassignHold 300
langevin on
langevinDamping 10.
langevinTemp $temp
langevinHydrogen on
#useFlexibleCell No
langevinPiston on
langevinPistonTarget 1.013
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temp
#******* integrator
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
#******* output
outputenergies 10
outputtiming 200
binaryoutput no
outputname $output
dcdfreq 100
XSTfreq 100
restartfreq 1000
#******* script
minimize 2000
run 2500000
#
#firsttimestep 214000
#numsteps 600000
*****************************************************************
Navratna Vajpai
Ph.D student in Prof. Stephan Grzesiek's group
NMR in Strukturbiologie,
Abt. Strukturbiologie & Biophysik,
Biozentrum,
CH-4056, Basel,
Switzerland
Phone - 0041 76 375 2003(M)
0041 61 267 2097(O)
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