On Fri, May 31, 2002, Antonio J. D?az Quintana wrote:
>
>
> We're trying to run NPT-MD using sander_classic in amber6.0. For doing
> that we preequilibrate the system using NVT-MD after minimizations.
> These
> steps seem to be correct. When we start NPT-MD, however, we have large
> oscillations in pressure. we set ref pressure to default value and
> we tryed several values of taup.
> I have two questions: How to solve such oscillations?
There is (probably) nothing to solve. See the FAQ:
http://amber.ch.ic.ac.uk/Questions/pressure.html
> Are the taup units in ps or in ps-1?
ps.
...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
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La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri May 31 2002 - 07:56:43 PDT
