Re: AMBER: Rotations about center of mass of an isolated system

From: David A. Case <>
Date: Mon, 14 May 2007 17:06:24 -0700

On Mon, May 14, 2007, Jennie Thomas wrote:
> Do you have another recommended way to start running an isolated
> water cluster to avoid this problem? Or, is this something I
> shouldn't worry about unless it actually results in an unphysical
> cluster geometry due to the rotations?

I don't know what is going on. Note that removing rotational motion
is "unphysical", not the reverse. Newton's equations conserve angular
momentum, so if you start with no angular momentum, it can only build up
by accumulation of error. You should be able to run nanoseconds of simulation
with nscm=0 and not encounter problems. (I would think,anyway: I've not done
a really comparable calculation myself.).

The system thinks that you don't have any overall rotational motion in your
simulation. So, you might want to be sure that your visual impression really
corresponds to overall rotation.


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Received on Wed May 16 2007 - 06:07:22 PDT
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