VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 09 2010 - 14:59:13 CST

hi irene,

On Tue, Mar 9, 2010 at 3:06 PM, Irene Newhouse <einew_at_hotmail.com> 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?

hmmm... have you tried using a fieldlines rep instead?
if you also colorize it by the potential, it can look much
better and more instructive than the potential as isosurface.
you have to be careful, though. this can be cpu time
demanding if you pick wrong parameters.

the other thing that worked well for me, is to map the potential
to a density map. i.e. use volmap tool to generate a radius
weighted density (perhaps with a scaling factor 1.5 or 2.0)
and then use the PME potential to colorize that and adjust
the isovalue of the density isosurface until you see what you
want to show. that had looked best for me, when using APBS
instead of PMEpot.

HTH,
   axel.

>
> Thanks!
> Irene Newhouse
>
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-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.