AMBER Archive (2005)

Subject: AMBER: Periodic box imaging using ptraj

From: Grzegorz Jezierski (jezierski_at_theochem.tu-muenchen.de)
Date: Tue Jul 26 2005 - 08:25:53 CDT


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,
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.

Thank you in advance,
Grzegorz

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu