Dear Dr. Case,
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 have thought that
nscm should set to 0 whenever ntt=3 is used. However, after checking
several tutorials using ntt=3
(
http://www.rosswalker.co.uk/tutorials/amber_workshop/), I found nscm is
set to 1000, the default value. Could you please clarify the usage of
this keyword again? I am thinking whether I need to redo my
calculations. Your kind assistance is highly appreciated.
Sincerely yours,
Shaowen
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, April 12, 2007 11:41 AM
To: amber.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
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Received on Wed Apr 18 2007 - 06:07:34 PDT
