-h [ --help ] display this help and exit --verbose be loud and noisy --verbose1 be very loud and noisy -v [ --verbose2 ] be extremly loud and noisy --top arg atomistic topology file
--cg arg coarse graining mapping and bond definitions (xml-file) --map-ignore arg list of molecules to ignore separated by ; --no-map disable mapping and act on original trajectory
--excl arg write atomistic exclusion list to file
--trj arg atomistic trajectory file --begin arg (=0) skip frames before this time (only works for Gromacs files) --first-frame arg (=0) start with this frame --nframes arg process the given number of frames
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