AMBER Archive (2002)

Subject: Re: the removal of global motion

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Nov 12 2002 - 17:52:41 CST

Hi,

Just another detail on the same topic.
If one sets NSCM=0 then the translational and rotational motion will NOT
be removed?
Is there a way for non-periodic simulations to remove only the rotational
or only the translational motion?

Thank you,
Ioana

****************************************************************************
* Ioana Cozmuta * *
* NASA-AMES Research Center * "Gravitation can not be held responsible*
* Mail Stop 230-3 * for people falling in love" *
* Moffet Field * *
* phone: (650) 604-0993 * Albert Einstein*
* fax: (650) 604-0350 * (1879-1955) *
****************************************************************************

On Tue, 12 Nov 2002, David A. Case wrote:

> 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
> ==================================================================
>
>