From: John Stone (
Date: Thu Jul 16 2009 - 11:32:50 CDT

  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.

  John Stone

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
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078