The mdout file has the potential energy for every ntpr snapshots. Those are
your sample points to create your probability density for your potential
energy.
--Jason
On Sat, Feb 26, 2011 at 12:31 AM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> How to get probability distribution of potential energies?
> Sorry that I can't find it in the mannual......
>
> On Sat, Feb 26, 2011 at 11:40 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > The temperature spread is based off of a relationship that maps energy
> > fluctuations to number of particles -- ensuring there is proper potential
> > energy overlap for a relatively high rate of exchanges to take place.
> The
> > temperatures generated by the website, if appropriate for GROMACS and
> other
> > force fields, should be a good starting place for Amber REMD as well.
> >
> > You can check this by running short simulations at each temperature and
> > then
> > histogramming the resulting potential energies to make sure that the
> > distributions overlap sufficiently.
> >
> > Hope this helps,
> > Jason
> >
> > On Fri, Feb 25, 2011 at 9:22 PM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> >
> > > Dear AMBER users,
> > >
> > > I found a website (http://folding.bmc.uu.se/remd/) for generating
> > > temperatures
> > > for REMD-calculations with the OPLS/AA force field and the GROMACS
> > > software.
> > >
> > > Is there any webserver providing tempteratures for REMD for AMBER
> users?
> > >
> > > Thanks!
> > >
> > > Sophia
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Feb 26 2011 - 08:00:02 PST
