Re: [AMBER] checking interaction between periodic images

From: Jason Swails <>
Date: Tue, 1 Mar 2011 08:29:33 -0500

It cannot. Each periodic image does exactly the same thing (i.e. when the
main system moves to the left, every periodic image moves to the left as
well). An atom's periodic image is always a full box-length away.

The only way I can really see a protein making a contact with its periodic
image is if you have a very long protein in a rectangular box in which one
of the dimensions of the protein is larger than the smaller side of the box
and the protein rotates, but this may cause problems in the simulation; I'm
not sure. In any case, I think this type of situation should typically be
avoided, since you're artificially hindering rotational behavior.

My last comment is that you can draw adjacent periodic boxes using VMD or
other molecular viewers. With VMD, go to Graphics -> Representations, then
there is a Periodic tab in the Representations window that will allow you to
draw periodic images in any of the 6 dimensions of a periodic box.

Hope this helps,

On Tue, Mar 1, 2011 at 5:37 AM, Bala subramanian

> Friends,
> Is there any way to check if the protein makes any contact with its
> periodic
> image during the simulation done with pbc.
> Thanks in advance,
> Bala
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Mar 01 2011 - 05:30:05 PST
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