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