Dear Rajendra,
The usual protocol consists in perform some time of NPT standard MD
simulation at the temperature of interest to achieve the correct density
and then preequilibrate several independent NVT replicas at your chosen
temperatures. Thus, start the REMD NVT production from these
pre-equilibrated replicas.
Alex.
On Wed, Mar 14, 2012 at 4:29 PM, 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
> >
> _______________________________________________
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>
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Received on Wed Mar 14 2012 - 09:00:03 PDT
