register_particles

mdhelper.openmm.system.register_particles(system: System, topology: Topology, N: int = 0, mass: float | Quantity = 0.0, *, chain: Chain = None, element: Element = None, name: str = '', resname: str = '', nbforce: NonbondedForce = None, charge: float | Quantity = 0.0, sigma: float | Quantity = 0.0, epsilon: float | Quantity = 0.0, cnbforces: dict[CustomNonbondedForce, tuple[Any]] = None) → None

Sequentially register particles of the same type to the simulation system, topology, and nonbonded pair potentials.

Parameters:

systemopenmm.System

OpenMM molecular system. Can be None if particles are to be registered to the topology only.

topologyopenmm.app.Topology

Topological information about an OpenMM system.

Nint, default: 0

Number of atom(s). If not specified, no particles are added.

massfloat or openmm.unit.Quantity, default: 0

Molar mass. If not specified, particles are massless and will not move.

Reference unit: \(\mathrm{g/mol}\).

chainopenmm.app.Chain, keyword-only, optional

Chain that the atom(s) should be added to. If not provided, a new chain is created for each atom.

elementopenmm.app.Element, keyword-only, optional

Chemical element of the atom(s) to add.

namestr, keyword-only, optional

Name of the atom(s) to add.

resnamestr, keyword-only, optional

Name of the residue(s) to add. If not specified, name is used if available.

nbforceopenmm.NonbondedForce, keyword-only, optional

Standard OpenMM pair potential object implementing the nonbonded Lennard-Jones and Coulomb potentials.

chargefloat or openmm.unit.Quantity, keyword-only, default: :code`0`

Charge \(q\) of the atom(s) for use in the Coulomb potential in nbforce.

Reference unit: \(\mathrm{e}\).

sigmafloat or openmm.unit.Quantity, keyword-only, default: :code`0`

\(\sigma\) parameter of the Lennard-Jones potential in nbforce.

Reference unit: \(\mathrm{nm}\).

epsilonfloat or openmm.unit.Quantity, keyword-only, default: :code`0`

\(\epsilon\) parameter of the Lennard-Jones potential in nbforce.

Reference unit: \(\mathrm{kJ/mol}\).

cnbforcesdict, keyword-only, optional

Custom pair potential objects implementing other non-standard pair potentials and their corresponding per-particle parameters.

Example: {gauss: (0.3 * unit.nanometer,)}, where gauss is a custom Gaussian potential obtained using mdhelper.openmm.pair.gauss().