Re: AMBER: momentum and periodic boundary condition

From: David A. Case <>
Date: Thu, 1 Mar 2007 08:52:00 -0800

On Wed, Feb 28, 2007, Wei Chen wrote:
> I am concerned about removing of linear and angular momentum of center of
> mass because I was warned to avoid flying ice cube effects. However, I found
> on the list that some people mentioned the angular momentum can not be
> removed with periodic boundary condition. I am wondering why?

Hard to answer simply, but (basically) the unit cell is rectangular, not
spherical, so there is no way to remove angular momentum in all cells without
really messing everything up.

> And I am using
> langevin dynamics thermostat. Some people said that it is not correct to
> remove the linear momentum of COM with langevin dynamics thermostat. Anybody
> knows the reason? How big is the effect to remove the linear momentum
> frequently with langevin dynamics thermostat?

Removing linear momentum violates the assumptions on which the Langevin
integrator is made. The most obvious symptom of this error is that the
average temperature does not match the target temperature, but there are
probably other more subtle problems as well. Note that amber does not allow
you to do this: for ntt=3, setting nscm to a non-zero value only affects the
coordinates, not the velocities.


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Received on Sun Mar 04 2007 - 06:07:40 PST
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