VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 09 2010 - 14:40:45 CST

Hi,
  Since PME is an inherently periodic calculation, it may be difficult to
prevent surfaces from extending across the periodic boundary. You could see
if drawing the surfaces with periodic images enabled gives you a better
image, this is done by enabling the check boxes in the "periodic" tab,
assuming that you've used the same periodic cell size for the PME calculation
in VMD and in your simulation. You can then use clipping planes to chop off
whatever parts you don't want shown. Beyond these suggestions, changing the
isovalue to select a more localized potential surface may also be helpful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 09, 2010 at 10:06:02AM -1000, Irene Newhouse wrote:
> I'm doing a PME Electrostatics calculation on a system. One of the
> isosurfaces wraps. I've tried many different combinations of selections in
> the setup box, but every single one ends up with a small part of the
> surface showing up at the opposite end of the box. Is there a trick for
> this, or should I just drop the value of the plot until it fits in the
> box?
>
> Thanks!
> Irene Newhouse
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078