AMBER Archive (2007)

Subject: RE: AMBER: nscm in simulation annealing

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Tue Apr 17 2007 - 11:26:01 CDT

 
Thank you very much, Dr. Case. I think I need to improve my English.
That helps me a lot.

Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Tuesday, April 17, 2007 11:18 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: nscm in simulation annealing

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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