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>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 http://folding.bmc.uu.se
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