[gmx-developers] Implementing Replica Exchange

[Peter Tieleman]

We're planning to implement replica exchange in the next couple of 
months in Gromacs.

Regards,
Peter

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!!)
>
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-- 
Dr.D. Peter Tieleman, Associate Professor, AHFMR Scholar
Dept. Biological Sciences, University of Calgary
2500 University Dr. NW, Calgary, Alberta T2N1N4 Canada
Fax: (403) 289-9311 Web: http://moose.bio.ucalgary.ca