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

[shivangi nangia]

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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