From: Josh Vermaas (
Date: Fri Jun 19 2020 - 15:47:22 CDT

Ok, I'm alot less familiar with material science applications. If these are
permanent bonds that VMD's automated topology picks up, I'd use the
numbonds selection I mentioned earlier. If instead they are fleeting, I
think you'd need to use measure contacts. Again, I don't know your system
well enough to understand what you are trying to quantify.


On Fri, Jun 19, 2020 at 10:51 AM Otakandza Glenn <>

> Hi Josh,
> It's in a plasma-surface interaction. I'd like to count the number of
> atomic bonds in the films formed on the surface.
> Le ven. 19 juin 2020 à 15:56, Josh Vermaas <> a
> écrit :
>> Any particular reason why this wouldn't work?
>> set sel [atomselect top "all"]
>> $sel get numbonds
>> That reports the number of bonds attached to each atom. Note however that
>> from xyz files, VMD guesses bond topologies from the first file loaded, and
>> never changes them, so if you are coming from a QM trajectory, this won't
>> do what you likely want to do. In what context do you want to count bonds?
>> -Josh
>> On Fri, Jun 19, 2020 at 4:37 AM Otakandza Glenn <>
>> wrote:
>>> Hi Dear developers,
>>> I would like to know how to count the number of atomics bonds when
>>> viewing with VMD for an xyz file.