Re: AMBER: Periodic box imaging using ptraj

From: Thomas E. Cheatham, III <>
Date: Tue, 26 Jul 2005 14:11:39 -0600 (Mountain Daylight Time)

> I ran a 2-ns of DNA in rectilinear water box. I had the wrapping option OFF
> (iwrap=0) throughout the entire run.
> After transforming my trajectory (generated by AMBER8) with ptraj, I am
> getting a strange box shape:
> * if I use command: "image center byres :WAT" - then I get something like two
> intersecting (at right angles) narrow boxes merged into one,
> or,
> ** if I use command: "image origin :WAT byres :*" - then I get a "nice"
> rectilinear box, but the solute is displaced out of the box. Other
> combinations of the above command produce either of these 2 types of system.
> Before I used AMBER6 with wrapping ON and didn't have this type of problem.

You likely need to image not only the waters, but everything else.
Additionally, if you have multiple solute molecules, these can become
separated as has been discussed extensively in the archives and tutorials
and/or the solute may diffuse out of the primary unit cell. If you image
only the waters, the solute may still be outside the primary unit cell.

Basically, to get back to the system you expect (i.e. solute surrounded
by solvent) you want to center your region of interest (solute) and then
image everything not just the waters (as in the commands above).

   center .P mass origin
   image origin center


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Received on Tue Jul 26 2005 - 21:53:01 PDT
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