The following table contains the input options for CSG,

Property Name

Default Value

Description

ident

Molecule name in reference topology.

topology

Section defining coarse grained beads of molecule.

topology.cg_beads

Section defining coarse grained beads of molecule.

topology.cg_beads.cg_bead

Definition of a coarse grained bead.

topology.cg_beads.cg_bead.name

Name of coarse grained bead.

topology.cg_beads.cg_bead.type

Type of coarse grained bead.

topology.cg_beads.cg_bead.mapping

Mapping scheme to be used for this bead (specified in
section mapping) to map from reference system.

topology.cg_beads.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.

topology.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.

topology.cg_bonded.bond

Definition of a group of bonds.

topology.cg_bonded.bond.name

Name of the bond.

topology.cg_bonded.bond.beads

List of pair of beads that define a bond. Names specified
in cg_beads

topology.cg_bonded.angle

Definition of a group of angles.

topology.cg_bonded.angle.name

Name of the angle

topology.cg_bonded.angle.beads

List of triples of beads that define a bond. Names specified
in cg_beads

topology.cg_bonded.dihedral

Definition of a group of dihedrals. Since the exact functional
form does not matter, this combines proper as well as
improper dihedrals.

topology.cg_bonded.dihedral.name

Name of the dihedral

topology.cg_bonded.dihedral.beads

List of quadruples of beads that define a bond. Names
specified in cg_beads

maps

Section containing definitions of mapping schemes.

maps.map

Section for a mapping for 1 bead.

maps.map.name

Name of the mapping

maps.map.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.