The XML topology root element, the base for the topology can be defined by the “name” attribute The following table contains the input options for CSG,

Property Name | Default Value | Description
--- | --- | ---
h5md_particle_group |  | Attribute name holds the name of particles group in H5MD file
molecules |  | The the molecules in the trajectory or other operation on the molecules.
molecules.molecule |  | Definition of the molecule, with attributes: name, nmols and nbeads. The name defines residue name, nmols tells how many times this molecule has to be replicated to match with trajectory file and nbeads defines number of beads in every molecule.
molecules.molecule.bead |  | Define the bead in the molecule. Attributes are: name - the name of bead, type - the type of bead, mass - the mass of bead, q - the value of charge and resid - the id of the residue the bead belongs to (>=1).
molecules.clear |  | Clear the information about the molecules
molecules.rename |  | Rename the molecules; attributes: “name” - the new name, “range” - the range where the new name will be set in the format start_range:end_range
molecules.define |  | Define the molecules; attributes: “name” - the name of molecule, “first” - the id of first molecule, “nbeads” - the number of beads in the molecule, “nmols” - the number of molecules
bonded |  | This section defines the topology of the molecules, it is used to generate proper exclusions for calculating rdfs
bonded.bond |  | Describes the bond
bonded.bond.name |  | The name of the bond
bonded.bond.beads |  | The pair of the beads in the format MOLECULE_NAME:BEAD_NAME
bonded.angle |  | Describes the angle
bonded.angle.name |  | The name of the angle
bonded.angle.beads |  | The triplet of the beads in the format MOLECULE_NAME:BEAD_NAME
bonded.dihedral |  | Describes the dihedrals
bonded.dihedral.name |  | The name of the dihedral
bonded.dihedral.beads |  | The quadruplet of the beads in the format MOLECULE_NAME:BEAD_NAME
beadtypes |  | Allows defining bead types
beadtypes.rename |  | Rename the bead type; attributes: “name” - the old name, “newname” - the new name
beadtypes.mass |  | Define the mass of the bead type; attributes: “name” - the bead type name, “value” - the new mass