From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 12 2010 - 14:59:44 CDT

Hi,
  I can look into adding this. Another approach would be to use GPU
acceleration for "within" and other computationally demanding selections.
That could make processing of trajectories of very large structures go
quite a bit faster. This particular case might be worth adding a new
keyword like "withinshell", since it would also require special atom
selection syntax for the extra radius parameter. I'll have to look at
how much trouble it will create for the atom selection parser.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 11, 2010 at 06:59:08PM +0200, jonathan wrote:
> Hi,
>
> I'm looking for some help to add a keyword in the VMD atom parser, which
> selects "layers" of molecules around a reference group. While the
> combination of two -within- selections works fine, it gets quite heavy
> on large trajectories ( ex : (within 12 of protein) and (not within 6 of
> protein)).
>
> Looking at the find_within_routine in the SpatialSearch.C, it seems that
> adding another parameter to the condition would do the trick.
> l.1113 if (dx2 + dy2 + dz2 < r2)
>
> But I'm not comfortable enough with the atom parser to do it.
> Got Hints ?
>
> Thanks !
>
> Jonathan
>
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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
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