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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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Fri Feb 25 2011 - 22:00:02 PST
