VMD-L Mailing List

From: Aman Jindal (amanjindal04711_at_gmail.com)
Date: Sun Mar 19 2017 - 06:01:28 CDT

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 ?

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.

Thanks in advance,
Aman