AMBER Archive (2006)

Subject: Re: AMBER: how to limit the simulation space

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Aug 28 2006 - 20:04:39 CDT

> 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?)

Bill
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