[gmx-users] Replica Exchange MD using Gromacs

[Justin A. Lemkul]

Quoting Monika Sharma <mon_sharma at research.iiit.ac.in>:

> Hi!!
> Thanks for suggestion. But still the problem is that whatever literature
> i have, I could just get the way that they just did replica exchange at
> these or that intervals. But still couldn't get clear the protocol of
> doing replica exchange using Gromacs. That's why i wished for some
> pieces of advice from the experts who have successfully implemented REMD
> using Gromacs.

I haven't done a lot of REMD, so if someone out there has better ideas about how
to do it, I hope they will add to what I'm going to tell you.

It is pretty simple to set up your MD runs to do REMD.  Make a set of .mdp
files, each specifying a different temperature that you wish to use.  Number
the output .tpr files according to index, from 0 to whatever (i.e., if you have
10 different temperatures you would have md0.tpr, md1.tpr...md9.tpr).

The interval for replica exchange is given by the mdrun flag -replex (refer to
the manual, it's all in there).  The -np flag for mdrun must agree with however
many .tpr files you have (i.e., 10 for the above general example using md0.tpr
through md9.tpr).  As was explained in a post just a few weeks ago,
nomenclature for the input is critical to getting mdrun to work.  Your command
line would be:

$ mdrun -s md.tpr -np 10 -replex (number of steps) (followed by whatever output
options)

That way, mdrun will find all of your md*.tpr files.

Hopefully this helps.  Again, I've only done a few REMD runs, so others may have
more details to add.

-Justin

> Thanks a lot..
> Regards,
> Monika
> On Fri, 2007-11-30 at 14:27 +0200, OZGE ENGIN wrote:
> > Hi Monica,
> >
> > I had not found a detailed tutorial about it; however, you can search for
> papers in which the simulations are performed via REMD.This will be helpful.
> >
> > Ozge.
> >
> > -----Original Message-----
> > From: "Monika Sharma" <mon_sharma at research.iiit.ac.in>
> > To: gmx-users at gromacs.org
> > Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST)
> > Subject: [gmx-users] Replica Exchange MD using Gromacs
> >
> > Dear All,
> >
> > I am trying REMD for the first time using Gromacs. But I am not finding
> > any much helpful material regarding the replica exchange using Gromacs.
> > Can anyone who has done REMD please let me know about any good tutorial
> > where I can understand the way this replica exchange work in gromacs and
> > the right protocol to do so..
> >
> > Thanks a lot in advance..
> >
> > Regards,
> > Monika
> > CCNSB, IIIT,
> > Hyderabad.
> >
> >
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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