Yes, *.gro files are not supported by OB, but there is nothing specific to CG in that format.
But OB do support *.xtc file format (read-only), which is "a compressed version of the trajectory, containing only coordinate, time, and box vector information". But I didn't find any other documentation about this in OB other than 'babel -Hxtc'. For it to be able to get bead radii, OB should be able to parse Gromacs topology files (there is already a request for that: http://sourceforge.net/tracker/?func=detail&aid=1583929&group_id=40728&atid=447448 altough the intent of the request is much wider than just the ability to read) or to read Gromacs run input files *.tpr (binary). I'm wondering maybe it is possible to deduce that it is a CG system from the distances to nearest neighbors? Or it might be possible to just introduce an option to deduce radii from distances (so that is optional feature). Cheers, Reinis S , 2010-05-29 15:42 +0400, Konstantin Tokarev rakstīja: > >Usually these models don't contain all atomic coordinates, but they can > >be used to coarse-grain the system (generate coordinate file with beads) > >and there are procedures to generate all atom coordinates from CG > >system. Probably drawing them in Avogadro also might be of some utility. > > >http://en.wikipedia.org/wiki/Molecular_dynamics#Coarse-graining_and_reduced_representations > > >I'm interested in using Gromacs for CG MD simulations. An example file > >in attachment (*.gro). It would be nice to be able to visualize MD > >trajectories for such simulations. > > I don't see support for Gromacs outputs on > http://openbabel.org/wiki/Category:Formats. Feel free to write feature > request for OpenBabel project, and post example file there. > > Maybe some additional data structure is needed in OB for correct storage of > CG systems, or they may be stored as usual atoms but with different radii and > some other properties which are usually taken from element-based tables > ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
