[gmx-users] Problem in Replica Exchange

[Mark Abraham]

----- Original Message -----
From: Nimesh Jain <nimeshjain2010 at u.northwestern.edu>
Date: Wednesday, August 4, 2010 1:48
Subject: Re: [gmx-users] Problem in Replica Exchange
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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.

The simulations are independent until exchange attempts occur, at which point they must communicate. So in principle, they could get out of step, but (in typical cases) not by very much. If you run the replica .tprs as non-replica simulations, you ought to see them all complete at about the same time.

I/O buffering can introduce a source of apparent asynchronicity. If a multiple simulation terminates unexpectedly, some files may have been flushed more recently than others, and give the appearance of longer progress.

Mark

> 
> Thanks for the help. All suggestions were really helpful.
 > 
> Thanks,
> Nimesh
> 
> 
> 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:
 > 
>      #!/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
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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
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 > 
> > 
> -- 
> Nimesh Jain
> Graduate Student
> Biomedical Engineering
> Northwestern University
 > -- 
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