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

From: David A. Case <>
Date: Mon, 14 May 2007 09:19:20 -0700

On Thu, May 10, 2007, Jennie Thomas wrote:
> I'm running an isolated small water cluster using Amber 8 (NVE
> ensemble). The cluster is rotating about the center of mass during
> the simulation run. I've tried to play with NSCM to remove both
> rotations and translations from the dynamics. But, there is still a
> collective rotational motion even setting NSCM=1. Any ideas why the
> collective rotations aren't being removed from the dynamics?

Do you get messages in the output about removal of translation and rotation?
Do these show very high energies or temperatures? If the water cluster
is fluxional, so that there is no average structure, it is certainly possible
that removing the instantaneous rotation about the current structure may not
do what you want. How are you deicding that collective rotations are not
being removed?


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Received on Wed May 16 2007 - 06:07:19 PDT
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