[gmx-developers] modifying replica exchange to allow Hamiltonian exchanges
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Mon Feb 28 00:14:48 CET 2011
> Ideally, one would like to have a single generalized HREX ensemble,
> yet with a possibility of decoupling vdW and Coulomb (up to three
> independent lambdas (I only need two at the moment)). This is in
> contrast to having to do (up to three) independent HREX runs.
This is already in the code scheduled for inclusion.
> now I am doing both changes (Coulomb and vdW) at the same time, which
> benefits from adjusting sc_alpha and sc_sigma slightly to get better
> acceptance ratios. I am mostly using your p=1 potential form.
I have discovered lots of problems doing this. When one moves to different
systems with different charges/LJ terms, the sc_alpha and sigma required to
get good exchange significantly. It is almost always more statistically
efficient to do coulomb linearly, then do vdw. p=1 is a good form to use.
> would like to have an option of having multiple independent lambdas
> for different residues when I have to mutate several in one structure.
We are planning to do this, but this is HIGHLY nontrivial. This will take a
while to get in. But it's definitely in the works.
> I would like to help test the implementation that is capable of
> nonlinear HREX against my script. Let me know if that would be of
I'll email you off list with more information.
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
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