On Tue, Nov 12, 2002, Shixiang Yan wrote:
> I have a question about the removal of global motion in Amber simulations.
> We found in the manual that six degrees of freedom of global motion could
> be removed periodically by setting NTCM/NSCM; however, as we discussed
> with others, it appears that the global rotation could not be removed in
> the periodic boundary simulation. I was wondering how Amber handles the
> global rotation, by freezing them or something else?
We tried to be as clear as we could in the Users' Manual (p. 93): "For
non-periodic simulations, after every NSCM steps, translational and rotational
motion will be removed. For periodic systems, just the translational
center-of-mass motion will be removed."
The word "just" in the last sentence was meant to convey that there is no
removal of rotational motion for periodic systems.
..hope this helps...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
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue Nov 12 2002 - 15:25:09 PST
