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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 1 23:54:07 CET 2007

David van der Spoel wrote:
> 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.

Wasn't there a rework of REMD planned to permit multiple processors per 
replica? Has that made it to CVS yet?

With the REMD code as it stands in 3.3.1, I'd agree with David's 
estimate. That's the kind of time it took me to implement a version of 
the hybrid solvation RE method of Okur et al., as described in JCTC 
2(2):420, and that required linking in a PB solver.


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