[gmx-users] Replica Exchange with Solute Tempering

HANNIBAL LECTER hanniballecter13 at gmail.com
Sun Oct 27 03:45:17 CET 2013

I had tried using gromacs-4.6.1 to perform solute tempering. If you go
through terakawa's paper you have to describe the lambdas corresponding to
the temperatures. In your topology file define the params corresponding  to
the two end states l=0 and l=1. Then define vdw, bonded and coulomb lambdas
in the mdp file. The format is very well described in the manual. Then just
the regular -replex syntax would perform solute tempering. However, the
free energy module required to perform this, is extremely slow.
On Oct 26, 2013 8:46 PM, "David Osguthorpe" <david.osguthorpe at gmail.com>

> 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
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