VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 15 2006 - 18:21:12 CDT
- Next message: ×ÞÑ©Çç: "about parameter "wrapAll""
- Previous message: Narender Singh Maan: "minimum distance b/w two atoms"
- In reply to: Narender Singh Maan: "minimum distance b/w two atoms"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
-- 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 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: ×ÞÑ©Çç: "about parameter "wrapAll""
- Previous message: Narender Singh Maan: "minimum distance b/w two atoms"
- In reply to: Narender Singh Maan: "minimum distance b/w two atoms"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]