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 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt <schm...@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 > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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