On Fri, Jun 21, 2002, Qing Zhang wrote:
>
> I want to accurately calculate a system's free energy
> using MM-PBSA method in Amber after Molecular
> dynamics. My question is how to give proper values for
> "taupt" at different stages of MD (heatup, constant
> pressure, ..., production dynamics)? "taupt" seems to
> have a large effect on the fluctuations of energies.
For the "production" part (where you are taking snapshots),
tautp should be fairly large (say > 2.0 ps), or (I think) even
better, make it effectively inifinite (i.e. set ntt=0).
In early equilibration stages, I often use shorter values (starting
as low as 0.5 ps during initial heating), but other values could
be used.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri Jun 21 2002 - 17:28:38 PDT
