AMBER Archive (2007)

Subject: RE: AMBER: nscm in simulation annealing

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Thu Apr 12 2007 - 12:53:18 CDT

Thank you very much, Dr. Case. I am using AMBER 9. However, I can not
find the restriction. With ntt=3, if I did not set nscm=0, the default
value is 1000.

Are there any references about removing the center of mass, for Langevin
heat bath and others, and gb simulation?

Thanks again. I have thought my question was evapourated.

Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, April 12, 2007 11:41 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: nscm in simulation annealing

On Thu, Apr 12, 2007, Hu, Shaowen (JSC-SK)[USRA] wrote:
>
> I tried to run some simulation annealing on a complex of a protein and

> DNA, with Langevin thermobath and igb=1. I have trouble to understand
> the function of nscm. If nscm=0, the temperature is well controlled.
> But if nscm=500 or 1000, as suggested by a tutorial, the temperature
> looks very strange....

What version of Amber are you using? 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).
This restriction was not present in earlier versions of the code.

With earlier versions of the code, you should set nscm, especially for
gb simulations.

....hope this helps...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu