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
|