[gmx-developers] modifying replica exchange to allow Hamiltonian exchanges

[Ilja Khavrutskii]

Hi Michael,

Thank you for letting me know that this is already in the works. I
would certainly be interested to try out the branch that you have with
the developing implementation of the Hamiltonian replica exchange
(HREX). My perl script works with generally non-linear Hamiltonians
with respect to lambda, so it does include both soft core potentials
(Coulomb and vdW).

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. Right
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. Also, I
would like to have an option of having multiple independent lambdas
for different residues when I have to mutate several in one structure.

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
value.

Best,
-Ilja