[gmx-users] Problem in Replica Exchange

[Nimesh Jain]

And the simulation is for 100ns.

On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain <
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:
>
> #!/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 <spoel at 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.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
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>
>
>


-- 
Nimesh Jain
Graduate Student
Biomedical Engineering
Northwestern University
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