From: Caro Miguel (
Date: Sat Apr 05 2014 - 01:36:34 CDT

Dear all,

I am trying to render an ab initio molecular dynamics simulation with VMD, using VASP's vasprun.xml file as input.

VMD decides which atoms are bonded at the beginning of the simulation and then keeps them bonded for the remainder of the run. The atoms in my system are interacting, and during the course of the simulation bonds are broken and created. However bonds are not updated by VMD and the initially bonded atoms remain connected by sticks (I'm using the CPK drawing method) even if they fall far apart.

I would like to achieve two things:

1) Get VMD to dynamically update bonds depending on interatomic distances

2) Define the interatomic distances at which a pair of atoms can be said to be "bonded" (i.e. define covalent/ionic radii)

Can this be done?

Thanks and regards,

Dr. Miguel Caro
Postdoctoral researcher
Department of Electronics
Aalto University, Finland