AMBER: Periodic box imaging using ptraj

From: Grzegorz Jezierski <>
Date: Tue, 26 Jul 2005 15:25:53 +0200

Dear AMBER users,
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,
** 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.

Thank you in advance,

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Received on Tue Jul 26 2005 - 14:53:00 PDT
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