Re: [AMBER] Replica Exchange

From: Logan Ahlstrom <logana.email.arizona.edu>
Date: Wed, 14 Mar 2012 08:34:59 -0700

For explicit solvent REMD, equilibration in the NPT ensemble in can be
performed for a few hundred picoseconds at 300 K before running REMD in NVT.

Paschek, D., H. Nymeyer, and A. E. Garcia. 2007. Replica exchange
simulation of reversible folding/unfolding of the Trp-cage miniprotein in
explicit solvent: on the structure and possible role of internal water. J.
Struct. Biol. 157:524533.

Sanbonmatsu, K. Y., and A. E. Garcia. 2002. Structure of Met-enkeph- alin
in explicit aqueous solution using replica exchange molecular dynamics.
Proteins. 46:225234.
Ahlstrom, L. S. and Miyashita, O. 2011. Molecular Simulation Uncovers the
Conformational Space of the lambda Cro Dimer in Solution. Biophys. J.
101:2516-2524.


On Wed, Mar 14, 2012 at 8:29 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> replica exchange at NPT is not currently supported in Amber. This is
> tricky, since in principle the system would boil at the high T normally
> used for REMD. Look at work by Garcia and others to see how this can be
> handled.
>
> On Wed, Mar 14, 2012 at 11:22 AM, Rajendra Sharma <rajenbiotech.gmail.com
> >wrote:
>
> > Dear All,
> >
> > In replica exchange simulations, is NPT simulations are possible for
> > equilibration followed by NVT for the production run?
> >
> > Sincerely,
> >
> > Rajendra Sharma
> >
> > On Wed, Mar 14, 2012 at 2:04 AM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> >
> > > Hi, Rajendra,
> > >
> > > try 'remd temperature' query in g**gle
> > >
> > > 2012/3/13 Rajendra Sharma <rajenbiotech.gmail.com>
> > >
> > > > Dear All,
> > > >
> > > > I have to perform explicit solvent replica exchange simulations on a
> > > small
> > > > peptide. I am not sure how to decide the number of replicas and
> > > > temperatures. It would be of great help ifi get a tutorial or
> > > publication
> > > > to perform the simulations.
> > > >
> > > > Sincerely,
> > > >
> > > > Rajendra
> > > >
> > > > --
> > > > Rajendra Sharma
> > > > Junior Research Fellow,
> > > > Computational Biophysics,
> > > > *National Center for Biological Sciences,*
> > > > (Tata institute of Fundamental Research)
> > > > India.
> > > > Mobile No. +91-9950675288
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Sincerely,
> > > Dmitry Mukha
> > > Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Rajendra Sharma
> > Junior Research Fellow,
> > Computational Biophysics,
> > *National Center for Biological Sciences,*
> > (Tata institute of Fundamental Research)
> > India.
> > Mobile No. +91-9950675288
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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>



-- 
Logan S. Ahlstrom
Ph.D. Candidate
Department of Chemistry and Biochemistry
University of Arizona
Miyashita Lab
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Received on Wed Mar 14 2012 - 09:00:03 PDT
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