VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Mar 12 2012 - 14:30:23 CDT

On Mon, Mar 12, 2012 at 1:43 PM, Andrew DeYoung <adeyoung_at_andrew.cmu.edu> wrote:
> 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

yes.

> 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.

these are outdated. VMD ships with the pbctools plugin
as an integrated part and most of the time using the command
"pbc box" is all you need to do. check out the docs at:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

> 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?

no conversion is needed. .xtc works as well, btw.

axel.

> Thank you very much for your time.
>
> Andrew DeYoung
> Carnegie Mellon University
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.