VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Mar 09 2010 - 15:56:22 CST

Thanks for the suggestions. Working with the Periodic tab didn't help. Adjusting the contour until it fits into a single unit cell seemed to lose a lot of information. I'm not so interested in mapping potential to the molecular surface, which conveys different information. So either I show only orientations that lack the wrapping, explain the wrapping, or try field lines.

 

Irene
 
> Date: Tue, 9 Mar 2010 15:59:13 -0500
> Subject: Re: vmd-l: Isosurface wraps in PME Electrostatics calc'n
> From: akohlmey_at_gmail.com
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
>
> 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
> >
> > ________________________________
> > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up
> > now.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
                                               
_________________________________________________________________
Hotmail: Trusted email with powerful SPAM protection.
http://clk.atdmt.com/GBL/go/201469227/direct/01/