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

Omer Markovitch omermar at gmail.com
Sat Oct 17 18:16:35 CEST 2009

What I do is visualize as trace. Than all the coarse-grained sphere
are connected. Hope it helps. Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905

On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt <schmidt at bit.uni-bonn.de>wrote:

> 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
> --
> 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
> http://www.csb.bit.uni-bonn.de
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