VMD-L Mailing List

From: Nitin Rathore (rathore_at_cae.wisc.edu)
Date: Fri Jun 18 2004 - 10:03:37 CDT

Hi,
I am trying to view the trajectories of my simulation that have been
written in Gromacs ".trr" format. The periodic boundary conditions are
giving me problems. Every time few sites of a molecule crosses one edge
of the box and re-enters from the opposite edge, VMD tries to create
bonds between the broken halves of the molecule. Since at any given time
there are enough water molecules that exist in this broken
configuration, VMD ends up creating a mesh of lines across the
simulation box.
Does anyone know how to fix this? Can anything be done without changing
the .trr files?

--Nitin
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Nitin Rathore
Graduate Research Assistant
Department of Chemical Engineering
University of Wisconsin-Madison.
http://www.cae.wisc.edu/~rathore
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