[gmx-users] Problem in Replica Exchange
nimeshjain2010 at u.northwestern.edu
Tue Aug 3 17:47:48 CEST 2010
My time step is 1 fs. And the md0.log doesn't have anything about replica
exchange which I suppose means that its not doing replica exchange.
In my other simulation, (100 ns duration and 1 fs time step), replica
exchange is initialized but the exchange frequency is 10^9 (so I am not
actually doing a replica exchange, but I have the conditions for that.)
Is it possible that the parallel replicas can go to different time steps
during the simulation if the simulation is a replica exchange one but no
exchanges are attempted during the duration of the simulation.
Thanks for the help. All suggestions were really helpful.
On Tue, Aug 3, 2010 at 10:23 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:
> 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
>> <nimeshjain2010 at u.northwestern.edu
>> <mailto: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:
>> #$ -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
>> 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 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.
>> 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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>> Nimesh Jain
>> Graduate Student
>> Biomedical Engineering
>> Northwestern University
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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