From: Axel Kohlmeyer (
Date: Sat Nov 27 2021 - 07:45:18 CST

Periodic display in VMD is done by replicating the visualization from the
principal cell.
Because of that, no bonds across periodic boundaries can be visualized.
If you want to see those, you will have to create a custom trajectory file
with the desired replicated positions and then visualize that.

On Sat, Nov 27, 2021 at 8:36 AM MD Simulation <>

> Hello,
> I'm running a reactive MD and would like to visualize the bonds using
> dynamic bonds but bonds are not handled across PBC. Are there any
> suggestions on dealing with bond formation across PBC?
> Thanks,
> Joe

Dr. Axel Kohlmeyer;!!DZ3fjg!p6xYKp6D-mwRLQ3PWJk5jodmw01KxzaGfK1iZsU9qvSpsFyXYGUYAdbeKXM9KFlcpQ$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.