On Wed, Mar 12, 2003, yuan bo wrote:
> I know that NDFMIN and NSCM options are to remove
> motion of mass center. But I would like to know what
> position them should be used in. Because in some MD
> references (mainly for amber4 and amber 5 version),
> removal of mass center often be found in computational
> methods. Now I use Amber 6 and simulate protein in
> non-aqueous solvent with periodic condition. Should I
> use the two option? in equilibration or in production
> simulation?
The NDFMIN value is now calculated automatically by the program. It doesn't
hurt to set the NSCM value (try 500 or so): if there is no COM motion,
it doesn't do anything; if there is some such motion, it will alert you
to a (potential) problem.
...good luck...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
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Mar 13 2003 - 05:53:01 PST
