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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Received on Fri Feb 25 2011 - 20:00:02 PST
