[gmx-developers] Implementing Replica Exchange

[Erik Lindahl]

Hi Senthil,

It's trivial since the individual simulations are essentially 
disconnected.

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. .

Cheers,

Erik


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!!)
>
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