cgexplore.forcefields.MartiniSystem

class cgexplore.forcefields.MartiniSystem(molecule, forcefield_terms, system_xml, topology_itp, vdw_bond_cutoff, bead_set)

Bases: object

Assign a system using martini_openmm.

Methods

get_openmm_system	Return OpenMM.System object.
get_openmm_topology	Return OpenMM.Topology object.

Attributes

molecule
forcefield_terms
system_xml
topology_itp
vdw_bond_cutoff
bead_set

Parameters:

• molecule (Molecule)

• forcefield_terms (dict[str, Sequence[Bond | Angle | CosineAngle | Torsion | tuple[int, int]]])

• system_xml (Path)

• topology_itp (Path)

• vdw_bond_cutoff (int)

• bead_set (BeadLibrary)

get_openmm_system()

Return OpenMM.System object.

Return type:

System

get_openmm_topology()

Return OpenMM.Topology object.

Return type:

Topology

bead_set: BeadLibrary

forcefield_terms: dict[str, Sequence[Bond | Angle | CosineAngle | Torsion | tuple[int, int]]]

molecule: Molecule

system_xml: Path

topology_itp: Path

vdw_bond_cutoff: int