[gmx-users] Problem in Replica Exchange

[David van der Spoel]

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:
>
>     #!/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 <mailto: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 <mailto:spoel at xray.bmc.uu.se>
>         http://folding.bmc.uu.se
>         --
>         gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at 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-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
>
>
> --
> 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