[gmx-users] Problem in Replica Exchange
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 3 17:23:12 CEST 2010
On 2010-08-03 17.17, Nimesh Jain wrote:
> And the simulation is for 100ns.
So you are trying exchanges ecery 2 ns (assuming 2 fs timestep). That is
rather long. If you check the file md0.log you can see whether the repl.
exch. code is initialized at all. If that is the case then I guess you
are seeing output file buffering (check dates on your files: the shorter
ones should be older). If not something else is wrong.
> On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain
> <nimeshjain2010 at u.northwestern.edu
> <mailto:nimeshjain2010 at u.northwestern.edu>> wrote:
> mdrun command I am using: (I have a shell script that adds jobs on
> the server) Following are the contents of that:
> #$ -cwd
> #$ -j y
> #$ -S /bin/bash
> #$ -pe mpi 8
> echo $TMP > info1
> unset SGE_ROOT
> cp $TMP/machines .
> $MPI_DIR/bin/mpirun -np $NSLOTS -machinefile $PWD/machines \
> /share/apps/gromacs-4.0.5/bin/mdrun_mpi \
> -s topol_.tpr -multi 8 -pd replex 1000000
> On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> On 2010-08-03 17.08, Nimesh Jain wrote:
> I am doing a replica exchange simulation with 8 replicas. I
> was looking
> at my data and I observed that a couple of replicas are
> around 10 and 20
> ns ahead of everything else. Is it normal or is this wrong ?
> Please let me know.
> What frequency of exchange do you use?
> Please give mdrun command line
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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> Nimesh Jain
> Graduate Student
> Biomedical Engineering
> Northwestern University
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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