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mapping

Please mind that dots in xml tags have to replaced by subtags, e.g. x.y has to be converted to x with subtag y.
  • cg_molecule
    • ident Molecule name in reference topology.
    • maps Section containing definitions of mapping schemes.
      • map Section for a mapping for 1 bead.
        • name Name of the mapping
        • weights Weights of the mapping matrix. Entries are normalized to 1, number of entries must match the number of reference beads in a coarse-grained bead.
    • name Name of molecule in coarse-grained representation.
    • topology Section defining coarse grained beads of molecule.
      • cg_beads Section defining coarse grained beads of molecule.
        • cg_bead Definition of a coarse grained bead.
        • cg_bead.beads The beads section lists all atoms of the reference system that are mapped to this particular coarse grained bead. The syntax is RESID:RESNAME:ATOMNAME, the beads are separated by spaces.
        • cg_bead.mapping Mapping scheme to be used for this bead (specified in section mapping) to map from reference system.
        • cg_bead.name Name of coarse grained bead.
        • cg_bead.type Type of coarse grained bead.
      • cg_bonded The cg_bonded section contains all bonded interaction of the molecule. Those can be bond, angle or dihedral. An entry for each group of bonded interaction can be specified, e.g. several groups (types) of bonds can be specified. A specific bonded interaction can be later on addressed by MOLECULE:NAME:NUMBER, where MOLECULE is the molecule ID in the whole topology, NAME the name of the interaction group and NUMBER addresses the interaction in the group.
        • angle Definition of a group of angles.
        • angle.beads List of triples of beads that define a bond. Names specified in cg_beads
        • angle.name Name of the angle
        • bond Definition of a group of bonds.
        • bond.beads List of pair of beads that define a bond. Names specified in cg_beads
        • bond.name Name of the bond.
        • dihedral Definition of a group of dihedrals. Since the exact functional form does not matter, this combines proper as well as improper dihedrals.
        • dihedral.beads List of quadruples of beads that define a bond. Names specified in cg_beads
        • dihedral.name Name of the dihedral