From: Axel Kohlmeyer (
Date: Fri Jun 18 2004 - 13:46:13 CDT

On Fri, 18 Jun 2004, John Stone wrote:

JS> Hi,
JS> It should be possible for you to wrap coordinates after-the-fact without
JS> modifying your .trr files at all. There's a script in the VMD script library
JS> that does this for trajectories produced by NAMD, with a little work it
JS> could be made to work for TRR files from Gromacs I suspect.
JS> Probably the best thing would be to modify that script to get the
JS> cell info from VMD rather than assuming the existence of an XST file
JS> ala NAMD. If someone has already done this, please let me know, otherwise
JS> perhaps I can take a look at doing this in a few weeks when I'm done
JS> with some more pressing work.

hi guys,

please try the attached version. it has worked for me, although
i have not found the time for a final review and clean-up to
resubmit it.

axel kohlmeyer.

JS> John Stone
JS> On Fri, Jun 18, 2004 at 10:03:37AM -0500, Nitin Rathore wrote:
JS> > Hi,
JS> > I am trying to view the trajectories of my simulation that have been
JS> > written in Gromacs ".trr" format. The periodic boundary conditions are
JS> > giving me problems. Every time few sites of a molecule crosses one edge
JS> > of the box and re-enters from the opposite edge, VMD tries to create
JS> > bonds between the broken halves of the molecule. Since at any given time
JS> > there are enough water molecules that exist in this broken
JS> > configuration, VMD ends up creating a mesh of lines across the
JS> > simulation box.
JS> > Does anyone know how to fix this? Can anything be done without changing
JS> > the .trr files?
JS> >
JS> > --Nitin
JS> > ============================================
JS> > Nitin Rathore
JS> > Graduate Research Assistant
JS> > Department of Chemical Engineering
JS> > University of Wisconsin-Madison.
JS> >
JS> > ============================================
JS> >

Dr. Axel Kohlmeyer                        e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum