On Mon, Nov 04, 2002, Craig A Bayse wrote:
> I having a little trouble with periodic boxes. During an MD simulation,
> the box does not remain uniform, the edges flare out such that it's no
> longer regular. I am using the input and pdb files from the DNA tutorial
> on the website, so I assume these would work properly. I have also tried
> to set boxes using setbox and set. What should I be doing?
You probably just need to "re-image" your system to move all atoms to the
central unit cell. See the "image" command in ptraj, or the iwrap variable
in sander.
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Nov 04 2002 - 10:32:11 PST
