AW: vmd-l: Finding particles that are close

From: Norman Geist (
Date: Tue Oct 08 2013 - 06:48:07 CDT

Hi Olaf,

the problem is, that VMD selections work based on atoms. So by using f.i. "all within 2 of all" you will create a list containing all atoms and compare to another list containing all atoms again. This results in measuring distances between all individual atoms, also to themselves, what of course come with distances of zero and VMD will show just everything you selected. But you can easily use the drawing method "dynamic bonds" for that purpose which has an modifiable cutoff to draw bonds between atoms inside that distance. Another option but less straight forward is to write a little tcl script that will for example loop over all atoms and use "within" to search in all atoms except the current looped atom for a given distance.

Best wishes

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Olaf Lenz
> Gesendet: Dienstag, 8. Oktober 2013 10:32
> An: VMD Mailing List
> Betreff: vmd-l: Finding particles that are close
> 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

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