On Thu, Jun 05, 2003, Shuang Ding wrote:
> In DNA tutorial the system is heated up at constant pressure. But I saw in
> this reflector it suggest that the system equilibrate to room temprature at
> constant volume before constant pressure simulation, why?
>
The DNA tutorial starts at 100K, and indeed heats up at constant pressure.
This apparently works in this case, but is still "dangerous", since it can
fail in some closely related instances. Definitely, if you start near 0 K,
turning on pressure coupling immediately can lead to crashes.
There is no "right" way to do equilibration, and (at least ideally), MD
results should be independent of how it is done. For that reason, different
people will have different ideas of how to go about this. I still think that
equilibrating to near the final temperature at constant V first is the "safer"
procedure.
...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
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La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Sat Jun 07 2003 - 00:53:01 PDT
