VMD-L Mailing List

From: Andrew DeYoung (adeyoung_at_andrew.cmu.edu)
Date: Mon Mar 12 2012 - 12:43:23 CDT

Hi,

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
(http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcbox/) exists
for drawing the simulation box. This script makes use of the PBCtools
package
(http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/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