VMD-L Mailing List

From: Olaf Lenz (olenz_at_Physik.Uni-Bielefeld.DE)
Date: Wed Feb 16 2005 - 03:08:15 CST

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Hello!

Xiongce Zhao wrote:
| I simulate a system with Periodic Boundary. The NAMD seems to use the
| infinite checkerboard for writing molecule positions in DCD file. It
| doesnot matter for simulation, but makes the movie ugly. Any one knows
| how to image the molecules back into the box ? Can this be done in VMD?

Yes, it can be done. On the VMD script page you'll find Jan Saam's
PBCwrap-script:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

To use this script, you'll need an XST-file. The script is well documented.

If you do not have an XST file, then you can also use my script
"olpcbwrap.tcl" that I've attached to this mail. It is inspired by Jan
Saams script, but expects the VMD-variables a, b and c to be set
correctly. The script is also well documented and I've already commited
it to the VMD people, but it does not show up on the script page so far.

Jan and I plan to merge the both scripts to provide a single one, but
we're not finished so far.

Cheers
        Olaf
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