[gmx-users] Replica Exchange with Solute Tempering

[David Osguthorpe]

On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote:
> Hi, all-
> 
> Rest essentially scales the solute-solvent interactions, but maintains
> the solute-solute interactions. This can be done solely with
> Hamiltonian replica exchange, which is in 4.6.  It's a bit tricky,
> though.  We plan on having something that does this automatically in
> 5.0 or 5.1, but it's not there yet.
> 
> What do you intend to do?  It could be that there's a better way to do
> what you want to do with Hamiltonian replica exchange, as well.
> 

Sorry - yes Im looking for an example of how to do REST via Hamiltonian
replica exchange

Ive seen the papers by Moors (Improved Replica Exchange Method for Native-State Protein Sampling)
and Terekawa (On easy implementation of a variant of the replica exchange with solute tempering in GROMACS)
and followed some of the gromacs user list discussions from 2011 on REST simulations

As you say, it looks like its "a bit tricky" so was hoping there was a toy example
somewhere

Thanks

David