VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 15 2006 - 18:21:12 CDT

Assuming I understant what you want, you'll want to run a doubly nested
loop searching for the minimum pair, from the atoms in the two residues.
You could use measure contacts to eliminate atoms beyond a certain
distance from the calculation, but the core code is a simple O(N^2)
loop over the number that have to be considered as potential minimal
distance pairs.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 15, 2006 at 06:05:30PM -0500, Narender Singh Maan wrote:
> Hi all, i am trying to list out the minimum distance between atoms(any) of
> two residues in a trajectory. Since the atoms (of these two residues) that
> are closest to each other keep changing in the simulation, i can't specify
> them, and hence having difficulty in doing what i want. I tried measure
> contacts, but again not getting what i want. Any suggestions would be of
> great help.
> thank you
> singh 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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