AMBER Archive (2007)

Subject: Re: AMBER: nscm in simulation annealing

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 17 2007 - 11:18:02 CDT

On Tue, Apr 17, 2007, Hu, Shaowen (JSC-SK)[USRA] wrote:
>
> Last week you wrote "Basically, center of mass motion should never be
> removed in Langevin simulations. In amber9, center-of-mass velocity
> removal is never done when ntt=3 (the system is just recentered every
> nscm steps, but the velocities are not altered)."

I'm not sure what it is that is unclear here. In Amber 9, no matter what
value of nscm you set, the velocities are never altered (at least, that is the
design). Every nscm steps, the *position* of the system is translated so that
its center of mass is at the origin. You can set nscm to 0 if you want, but
you run the risk in a very long simulation that the molecule will diffuse away
to very large values of the coordinates, and overflow can occur in the restart
and trajectory files.

....hope this helps...dac

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