From: Navratna Vajpai (navratna.vajpai_at_unibas.ch)
Date: Sun Jul 31 2005 - 02:27:57 CDT
> 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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