From: Fernando Vallejos-Burgos (
Date: Fri Oct 07 2016 - 06:03:34 CDT

For the first, refer to pbc tools: <>

For the second, in the VMD main menu: Mouse -> Labels -> Bonds (or angles)…. then click in the atoms

Dr. Fernando Vallejos-Burgos
Researcher at Center for Energy and Environmental Science
Shinshu University, Wakasato, Nagano 380-8553, Japan
Personal web: <>
Research group web: <>

> On 2016 Oct 7, at 15:03, Harish Srinivasan <> wrote:
> How is it possible to get a cubic or non-cubic box (my simulation box or a custom box) to be seen in the VMD graphics window along with my atoms ? Is there are also a possible way to click on the atoms and find distance between them or angle between three of them etc ?
> Thank you,
> Harish