VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Tue Oct 08 2013 - 10:24:22 CDT

Hello John
This is a command that I have used and have been a little confused about. Unfortunately I don't understand the two sentence documentation that goes with it. For instance I have two residues that I would like to measure the contacts between. Two lists are returned. { atmIndx1Res1 atmindx2Res1 ... } { atm1indxRes2 atm2indxRes2 ...}. now if I had three residues in my selection would the third set of numbers still be a list of atoms that were within a cutoff distance of residue 1 that reside in residue 3?

Brian

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of John Stone [johns_at_ks.uiuc.edu]
Sent: Tuesday, October 08, 2013 6:51 AM
To: Olaf Lenz
Cc: VMD Mailing List
Subject: Re: vmd-l: Finding particles that are close

Olaf,
  How about using "measure contacts"?
You can provide a specific distance criteria for measure contacts,
and that might do the trick.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 08, 2013 at 10:31:45AM +0200, Olaf Lenz wrote:
> Hi!
>
> For a tutorial, I wanted my students to visualize all pairs of particles
> in a system that are closer than a given distance $a$. I thought this to
> be a simple application of "within" selection, something like:
>
> exwithin 1 of all
>
> Unfortunately, this will not show anything. Finally, I noticed that it
> is not actually that simple, and I was not able to solve the problem.
> Does anybody have an idea how to do that? It would be really useful!
>
> Olaf
> --
> Dr. rer. nat. Olaf Lenz
> Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
> Phone: +49-711-685-63607 

--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/