Re: AMBER: Periodic box imaging using ptraj

From: Grzegorz Jezierski <>
Date: Wed, 27 Jul 2005 11:27:24 +0200

I'm still getting this cross-shaped box.
I typed (my DNA molecule consists of res.# 1-18):
center :1-18 mass origin
image origin center

Typing" "center .P mass origin" instead of "center :1-18 mass origin"
produces the same result.
Thank you.

Thomas E. Cheatham, III wrote:

>> 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
> --tom
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Received on Wed Jul 27 2005 - 10:53:00 PDT
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