From: Andrew DeYoung (
Date: Mon Mar 12 2012 - 12:43:23 CDT


Is there a way to draw (and dynamically update) the simulation box from a
Gromacs simulation? For example, I am running NPT simulations in Gromacs,
in which the box size is allowed to vary. I would like to visualize the
expansion and contraction of the simulation box over the course of the
trajectory. Is this possible? I am currently using Gromacs .trr files as
my trajectories, but I can easily convert this to the Gromacs .trj or .g96
file formats.

I see that a script
( exists
for drawing the simulation box. This script makes use of the PBCtools
However, it seems that these codes only read CHARMM and NAMD trajectories.

Do you have any experience in drawing the simulation box from a Gromacs
trajectory? Or is it possible to convert a Gromacs trajectory to a CHARMM
or NAMD trajectory?

Thank you very much for your time.

Andrew DeYoung
Carnegie Mellon University