>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 -- Regards, Konstantin ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
