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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Received on Wed Mar 14 2012 - 08:30:02 PDT
