From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Sun Jul 31 2005 - 11:17:20 CDT
Hi,
This may give you a few ideas about what the problem might be:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1317.html
Also, regarding your PMEGridSize parameters, some would suggest using a
larger value, especially in the X direction (in your case):
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0051.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1825.html
Would you please clarify your second question?
Blake
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Navratna Vajpai
Sent: July 31, 2005 3:28 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: running on two different machines....
From: Navratna Vajpai <navratna.vajpai_at_unibas.ch>
Date: July 31, 2005 9:24:39 AM CEST
To: namd-l_at_ks.uiuc.edu
Subject: running on two different machines....
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)
*****************************************************************
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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