[gmx-users] Coarse-Grain: GROMACS bond information to VMD

Thomas Schmidt schmidt at bit.uni-bonn.de
Fri Oct 16 11:24:00 CEST 2009

Dear all,

is there any possibility to give the bond information out of GROMACS
files to VMD? Especially for coarse-grained models (using the MARTINI
FF) this would be a nice feature for visualization.

But in that case the distance analysis doesn't work, because we will
always have too high distances between two particles (CG scale). If I
use "Dynamic Bonds" (as described in this thread:
http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html) VMD draws bonds also between non-bonded particles.

I know that there is no official solutions for this
(http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD), but maybe
anybody of you has a script to convert *.top/*.itp/*.rtp files with a
corresponding *.gro file into the PDB format with connectivity section
or into the (NAMD) *.psf format. (?)
The solution that I've found (top2psd.pl) is not smart enough because
it's a simple 1-to-1 conversion of GROMACS topology files and has not
the ability to replicate (and renumber) the topological data of single
molecules (http://baaden.free.fr/soft/compchem.html).

Thanks for your help...

Thomas H. Schmidt, PhD student
Computational Structural Biology
Chair of Life Science Informatics, B-IT
LIMES-Institute, University of Bonn
Dahlmannstrasse 2, D-53113 Bonn, Germany

Phone: +49-(0)228-2699 323
Fax: +49-(0)228-2699 341

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