From: Leandro Martínez (
Date: Thu Sep 25 2008 - 14:51:00 CDT

Hi Ananyo,
You probably want to wrap your coordinates, use
the PBCtools for that:


On Thu, Sep 25, 2008 at 3:29 PM, Ananyo Bandyopadhyay <>wrote:

> Hi all
> Can somebody guide me of how to make a cuboid box in VMD? I am making
> amorphous polymers with periodic boundary conditions (20 angstroms length
> along each axis) but when I am seeing the molecules in VMD, the box does not
> show up. I want the box so that the molecules appear to be inside a box of
> finite volume and not just scattered in space.
> Thanks and regards
> Ananyo.
> PhD student
> Department of Materials Sciences and Engineering
> Michigan Technological University