Nimesh Jain 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


You're not actually doing replica exchange. The proper flag is -replex, but since mdrun doesn't fail when it finds unknown options (like "replex"), it's just happily running multiple simulations. You're also only attempting an exchange every million steps, so unless your time step is exceptionally small, you may not get very good exchange between your replicas.

-Justin


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.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org
    <mailto: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
    <mailto:gmx-users-requ...@gromacs.org>.
    Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
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

Reply via email to