[gmx-users] REST2 swapping/exchange implementation in GROMACS

[Mark Abraham]

Hi,

Just as with temperature REM, at the intervals you choose, the simulation
will stop and adjacent replicas will do a Metropolis check for whether
their configurations are representative of the conditions in the other
simulations. The principle is independent of what varies across replicas.

Mark

On Wed, Aug 24, 2016 at 12:54 AM shivangi nangia <shivangi.nangia at gmail.com>
wrote:

> Dear Mark,
>
> Sorry about posting in the wrong mailing list.
>
> I understand that when implementing REST2 in GROMACS I am generating
> replicas through various lambdas.
> These replicas will run at same temperature say at 300 K and will only have
> an "effective temperature".
>
> [a-The lambdas will vary from 0 (low T) to 1 (High T),
> b- the charges, epsilon values and k values are scaled in a dual topology
> file]
>
> What I was confused about is will/how there be an "exchange" in these
> replicas?
>
> kindly advice.
>
>
> Many thanks in advance,
> sxn
>
>
> On Tue, Aug 23, 2016 at 6:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Please do not post questions about how to use GROMACS to the
> gmx-developers
> > mailing list, which is for questions about how to write code related to
> > GROMACS.
> >
> > On Tue, Aug 23, 2016 at 8:29 PM shivangi nangia <
> shivangi.nangia at gmail.com
> > >
> > wrote:
> >
> > > Hello,
> > >
> > > I have a question regarding implementing REST2 in GROMACS as suggested
> > in:
> > > (
> > > On easy implementation of a variant of the replica exchange with solute
> > > tempering in GROMACS, J Comput Chem. 32, 1228-1234, 2010).
> > >
> >
> > There's a rather full explanation of what is going on in that paper. I
> > trust you've read and understood it.
> >
> >
> > > How does the gromacs machinery know how to carry out the
> > exchange/swapping?
> > >
> >
> > The Hamiltonian (ie lambda) differs between replicas.
> >
> >
> > > the -replex probably will generate copies of the system at higher
> > > temperature which I do not want.
> > >
> >
> > You're assuming replica exchange means temperature REM, which is not what
> > that paper is talking about.
> >
> > Mark
> >
> >
> > > Kindly reply.
> > >
> > > Thanks in advance.
> > >
> > > sxn
> > > --
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