molsysmt.third_party.openmm.forces.add_allowed_z_region

molsysmt.third_party.openmm.forces.add_allowed_z_region(molecular_system, selection='all', z0='0.0 nm', width='1.0 nm', force_constant='5000 kilojoules_per_mole/nm**2', pbc=False, return_force=False, syntax='MolSysMT', skip_digestion=False)

Adding repulsive restraints confining particles within an allowed z-coordinate interval 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.

• z0 (object, default='0.0 nm') – Argument z0.

• width (object, default='1.0 nm') – Argument width.

• force_constant (object, default='5000 kilojoules_per_mole/nm**2') – Argument force_constant.

• pbc (bool, default=False) – 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 confining force instance.

Return type:

openmm.CustomExternalForce

Added in version 1.0.0.