AMBER Archive (2006)

Subject: Re: AMBER: Confusion about PBC

From: Thomas Steinbrecher (
Date: Wed Nov 29 2006 - 10:40:05 CST

Hi Anna,

did you try to wrap the coordinates back into the original box with ptraj?
water molecules diffuse to the neighboring boxes during a long simulation,
so that it will look like a fuzzy globular shell of waters, although
periodic boundary condition really are in effect and the wrapped
coordinates correspond to a closely packed box.

If this is the sole reason for your problem, then it is just cosmetic,
your simulation did the right thing.

Running this ptraj script will give you a better looking trajectory:

trajin <name>
center :<your solute residues> mass origin
image origin center
trajout <name>_img



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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