Mapping atomistic systems to coarse-grained systems Using MDTraj libraries and user-defined mapping files, convert an atomistic trajectory to a coarse-grained trajectory. Currently only support gromacs file formats.
Mapping files can be custom-named, but adding to the dict "all_cg_mappings" requires the keys (residue names) to correspond to residue names found in the atomistic trajectory. Values correspond to the mapping file.