RE: AMBER: nscm in simulation annealing

From: Hu, Shaowen (JSC-SK)[USRA] <"Hu,>
Date: Tue, 17 Apr 2007 11:59:43 -0500

Dear Dr. Ross Walker,

Thank you very much for your elaborate explanation. That helps me a lot.
I am learning AMBER slowly.


-----Original Message-----
From: [] On Behalf
Of Ross Walker
Sent: Tuesday, April 17, 2007 11:26 AM
Subject: RE: AMBER: nscm in simulation annealing

Dear Shaowen,

> 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
> (, 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.

The issue with removing center of mass in langevin simulations is a
theoretical one. If you regularly remove center of mass motion you will
not get the correct ensemble and things like diffusion coefficients etc
will be incorrect. You should read up on the langevin method in the
literature to be sure you understand the theory.

With regards to the keyword nscm the behavior is as follows:

1) When ntt /= 3
   default nscm=1000
   Center of mass translation and rotation is removed from the system
every nscm steps. After the first initial correction each subsequent
correction should be small simply coming from net translation introduced
by the thermostat. If you are running NVE the corrections should be VERY
small representing simply the errors inherent in the integration method.

2) When ntt == 3
   default nscm=1000
   Every nscm steps the coordinate system is recentered. Thus your
system can have center of mass motion but since in a very long
simulation the system could drift many hundreds of angstroms we don't
want it to diffuse so far that we overflow what the trajectory file can
handle. This also makes visualization of the trajectory file easier. In
the output file the amount by which the origin of the coordinates had to
be shifted to recenter the system is printed. This therefore correctly
implements the langevin method.
You could later postprocess the trajectory file to remove the origin
recentering if you so wished. Alternatively in calculating properties
such as diffusion coefficients since the amount of movement is written
to the output file so you can correct for this in your calculations.

  Alternatively if you want you can set nscm=0 in which case no
recentering will be done. However with a very long simulation you would
see your system translate a long way from the starting coordinates.

  With ntt=3 if you take the nscm=1000 simulation and post process the
trajectory to account for the recentering of the origin as specified in
the output file you will end up with the exact same trajectory as if you
set nscm=0.

I hope that clarifies things.

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Apr 18 2007 - 06:07:35 PDT
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