[gmx-users] Replica Exchange with Solute Tempering

[Andrew Ritchie]

Greetings,
I would also be interested in an example of using REST via Hamiltonian REMD
in the current gromacs build.  I'm particularly interested in enhanced
conformational sampling of 160-270 residue proteins. As it stands, I've
been unable to achieve any appreciable exchange probability in coulomb or
vdw lambdas without resorting to changing the lambda values by +/- 0.02 or
less and am hoping ST will allow me to increase the spacing between lambdas.
Thanks for any help,
Andrew


On Sat, Oct 26, 2013 at 9:45 PM, HANNIBAL LECTER <hanniballecter13 at gmail.com
> wrote:

> Hi
> 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>
> wrote:
>
> > 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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-- 
-Andrew Ritchie