molsysmt.third_party.openmm.forces.pin_atoms

molsysmt.third_party.openmm.forces.pin_atoms(molecular_system, selection='all', force_constant='5000 kilojoules/(mol*nanometers**2)', pbc=True, return_force=False, syntax='MolSysMT', skip_digestion=False)

Pinning selected atoms to fixed Cartesian positions using harmonic restraints in OpenMM.

Parameters:

• molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

• selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

• force_constant (object, default='5000 kilojoules/(mol*nanometers**2)') – Argument force_constant.

• pbc (bool, default=True) – Whether to take periodic boundary conditions into account.

• return_force (object, default=False) – Argument return_force.

• syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

• skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

The added pinning restraint force instance.

Return type:

openmm.CustomExternalForce

Added in version 1.0.0.