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
<nimeshjain2...@u.northwestern.edu
<mailto:nimeshjain2...@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:
#!/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
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.
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Nimesh Jain
Graduate Student
Biomedical Engineering
Northwestern University
--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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