AMBER Archive (2007)

Subject: Re: AMBER: nscm in simulation annealing

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 12 2007 - 11:41:03 CDT

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 

-- 

==================================================================
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.         |  skype:                 dacase
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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