AMBER Archive (2006)

Subject: AMBER: how to limit the simulation space

From: Eric Hu (
Date: Mon Aug 28 2006 - 19:55:11 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.

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