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:
#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -pe mpi 8
echo $TMP > info1
unset SGE_ROOT
cp $TMP/machines .
MPI_DIR=/opt/openmpi/
$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.
-Justin
Thanks,
Nimesh
On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
On 2010-08-03 17.08, Nimesh Jain wrote:
Hi,
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.
Thanks,
Nimesh
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.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
http://folding.bmc.uu.se
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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