[gmx-developers] Implementing Replica Exchange
spoel at xray.bmc.uu.se
Fri Sep 19 23:43:43 CEST 2003
On Fri, 2003-09-19 at 23:18, Erik Lindahl wrote:
> Hi Senthil,
> It's trivial since the individual simulations are essentially
> Just run the simulations in parallel for N steps. Check the results,
> exchange if necessary, and start new simulations.
> Actually, I would probably recommend implementing it as a higher-level
> script that calls the gromacs programs, so you can parallelize each of
> the underlying replica simulations independently. Otherwise you'll get
> a complicated two-layer situation if you are running e.g. 8 simulations
> in parallel where each of the simulation wants to use MPI independently
> of the others. .
actually it is mainly implemented (except for the replica bit).
will start N simulations with topologies topXXX.tpr and rename all the
other output likewise. It is currently only useful in special cases but
if you implement the communication of coordinates (for which there are
routines already) it should be quite straightforward.
> On Friday, September 19, 2003, at 02:07 PM, Senthil Kandasamy wrote:
> > Hi Developers,
> > I am interested in doing some replica exchange md simulations of
> > lipid/peptide systems.
> > How easy or difficult do you think will it be to implement it in
> > GROMACS?
> > I would probably have 8 replicas, each at a different temperature,
> > exchanging configurations for enhanced sampling.
> > Ideally, there would be one replica per processor, with communication
> > between processors happening every n (
> > ~100) steps, to attempt exchanges.
> > So communication is rather limited and it should not affect the
> > efficiency.
> > I know of people who do REMD using both CHARMM and AMBER.
> > So I guess implementing it in GROMACS should not be THAT difficult.
> > Any ideas? If the developers think that it is not that difficult, I
> > can devote most of my time to doing this.
> > Or else, I will just switch to AMBER for this particular problem, I
> > think. (sigh!!)
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-developers-request at gromacs.org.
> gmx-developers mailing list
> gmx-developers at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gmx-developers