VMD-L Mailing List

From: Chris Knorowski (cdknorow_at_iastate.edu)
Date: Tue Oct 08 2013 - 16:05:38 CDT

The easiest way to do is what Axel suggested using dynamic bonds. In the
GUI you can use dynamic bonds under graphics > representation> Drawing
Method > Dynamic bonds. Then set the cutoff distance to whatever you want
to.

Chris

On Tue, Oct 8, 2013 at 10:24 AM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

> 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/
>
> 

-- 
Christopher Knorowski
Iowa State Physics Department