And the simulation is for 100ns. On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain < 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 > > 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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern University
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