[gmx-users] Problem in Replica Exchange
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 3 17:21:44 CEST 2010
Nimesh Jain 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
You're not actually doing replica exchange. The proper flag is -replex, but
since mdrun doesn't fail when it finds unknown options (like "replex"), it's
just happily running multiple simulations. You're also only attempting an
exchange every million steps, so unless your time step is exceptionally small,
you may not get very good exchange between your replicas.
> 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
> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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