Re: the removal of global motion

From: David A. Case <>
Date: Tue 12 Nov 2002 15:25:09 -0800

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:
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            |
Received on Tue Nov 12 2002 - 15:25:09 PST
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