Re: problem of mass center

From: David A. Case <>
Date: Wed, 12 Mar 2003 21:02:10 -0800

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:
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:                   
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Received on Thu Mar 13 2003 - 05:53:01 PST
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