Re: taupt: time constant for heat bath coupling for the SOLUTE

From: David A. Case <>
Date: Fri 21 Jun 2002 17:28:38 -0700

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:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Fri Jun 21 2002 - 17:28:38 PDT
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