AMBER Archive (2005)

Subject: Re: AMBER: periodic boundaries and repeating structure

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Apr 14 2005 - 13:13:48 CDT

> With setBox center or vdw, my structure won't be replicated properly. Those
> options would add spaces and create edge effects.
> What else can I do?

You could write a new setBox option to determine box boundaries
that maximize the amount of unhindered interpenetration.

Possibly you could use belly or cartesian restraints to hold everything
fixed, then run low-temperature constant pressure and see if the box
shrinks. Best to visualize the result to validate that the box is
properly located.

Bill
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