AMBER Archive (2008)

Subject: Re: AMBER: peptide at the box center during NVT-MD

From: David A. Case (case_at_scripps.edu)
Date: Mon May 26 2008 - 11:09:51 CDT

On Mon, May 26, 2008, Darek Czapiewski wrote:
>
> I would like to keep my peptide at the box center during the NVT-MD
> simulation. Well, what should I do?

Why do you want to do this? Your system is periodic: there is no distinction
between the "center" of the box and the "edge" of the box. I certainly never
worry about such things, and cannot offhand think of any physical reason to
add an artificial constraint to an artificial point in space (the "center").

...dac

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