Re: AMBER: how to limit the simulation space

From: Bill Ross <>
Date: Mon, 28 Aug 2006 18:04:39 -0700 (PDT)

> Hi, I am trying to run a md for a small molecule in vacuum. I find
> that the molecule jumps around a lot and even escapes outside the
> virtual box that leads to a sander bomb. I wonder if there is a way to
> assign a potential well (grid box idea) so that whenever the molecule
> touches the wall, it will bounce back. Thanks.

You could remove center-of-mass motion periodically (NSCM?)

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Received on Wed Aug 30 2006 - 06:07:13 PDT
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