[gmx-developers] Energy and Foreign Lambdas and Hamiltonian Replica Exchange

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 1 23:01:47 CET 2007

Matt Wyczalkowski wrote:
> Hi,
> I'm investigating the feasibility of implementing Hamiltonian Replica 
> Exchange in Gromacs, so that swaps exchange lambda values (rather than 
> temperatures).  To do this, it is necessary to know energies for a given 
> configuration at other lambda values.  This is an issue which was 
> discussed a number of months ago in the context of the Bennett 
> Acceptance Ratio.
> Before delving in too far into the code, I wanted to get a feel for the 
> current state of development with respect to energy evaluations at 
> different lambdas, as well as whether Hamiltonian Replica Exchange has 
> been considered and/or implemented.  How significant an undertaking 
> would a generalization of Replica Exchange to allow for lambda swaps be?
> Thanks for your time --
> Matt
I'd say a couple of weeks to get it right. You can learn quite a bit 
from the current REMD implementation, but you'd need extra energy 
evaluations. Check the wiki, to see if this is there already, something 
similar is, anyway.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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