From: Axel Kohlmeyer (
Date: Sun Mar 19 2017 - 10:55:51 CDT

On Sun, Mar 19, 2017 at 7:01 AM, Aman Jindal <>

> Dear Users,
> I have a trajectory file from which I want to calculate the coordination
> no. of say type O atoms. I can replicate a frame (using topotools command)
> and calculate the coordination no. exactly for all the atoms including
> those which lie on the surface. But I want to do this over all the frames
> to get the average coordination no. of each one.
> Is there any way to replicate a trajectory in VMD ?

not directly, ​you would have to write a ​custom script or modify the one
in topotools to do what you want.

> I tried it after displaying the system periodic in all +-x,y,z directions,
> but the command in the tcl script like "within 3 of index 10" does not
> account for the atoms outside the original simulation box.

​the periodic visualization does not replicate the atom data internally,
but replicates the visualization after it has been realized.

however, there is an option in the atomselect syntax called "pbwithin"
instead of "within" and that might just do what you are looking for, even
without replicating the trajectory data.

axel. ​

> Thanks in advance,
> Aman

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.