VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 16 2009 - 11:32:50 CDT

Bin,
  The "within" commands in VMD use a spatial decomposition to
accelerate the search. You can find the related code in
SpatialSearch.[Ch] in the VMD source tree.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 16, 2009 at 09:29:43AM -0700, BIN ZHANG wrote:
> Dear all:
>
> Can someone tell me or point me a reference about the algorithm used
> to implement *within* command in VMD? I'm trying to do similar thing
> by calculating the distance between all atom-pairs, which is really
> really slow...
>
> Thanks,
>
> Bin 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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