AMBER Archive (2004)

Subject: Re: AMBER: distance between images

From: Bill Ross (
Date: Thu Oct 14 2004 - 10:09:11 CDT

> is there any routine to calculate the minimum distance between two images of
> the solute during an MD trajectory? I'm using a truncated octahedron box, and
> would like to check whether the protein in the box is interacting with its
> image(s).

Carnal's DISTRIBUTION DIST option handles the truncated octahedron box.
Ptraj might as well - try a measurement and see.

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