molsysmt.thirds.openmm.forces package#

Submodules#

molsysmt.thirds.openmm.forces.add_allowed_plane_region module#

molsysmt.thirds.openmm.forces.add_allowed_plane_region.add_allowed_plane_region(molecular_system=None, selection='all', force_constant='5000 kilojoules_per_mole/nm**2', point='[0,0,0] nm', normal_vector=[0, 0, 1], width='1.0 nm', pbc=False, return_force=False, syntax='MolSysMT', skip_digestion=False)[source]#: Add a flat-bottom restraint confining atoms near a reference plane.

molsysmt.thirds.openmm.forces.add_allowed_z_region module#

molsysmt.thirds.openmm.forces.add_allowed_z_region.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)[source]#: Convenience wrapper adding a plane restraint perpendicular to z.

molsysmt.thirds.openmm.forces.add_constant_force module#

molsysmt.thirds.openmm.forces.add_constant_force.add_constant_force(molecular_system, selection='all', force='[500,0,0] kilojoules/(mole*nanometer)', return_force=False, syntax='MolSysMT', skip_digestion=False)[source]#: Apply a constant external force to a selection of atoms.

molsysmt.thirds.openmm.forces.add_forbidden_plane_region module#

molsysmt.thirds.openmm.forces.add_forbidden_plane_region.add_forbidden_plane_region(molecular_system=None, selection='all', force_constant='5000 kilojoules_per_mole/nm**2', point='[0,0,0] nm', normal_vector=[0, 0, 1], width='1.0 nm', pbc=False, return_force=False, syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.thirds.openmm.forces.add_forbidden_z_region module#

molsysmt.thirds.openmm.forces.add_forbidden_z_region.add_forbidden_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)[source]#

molsysmt.thirds.openmm.forces.add_harmonic_bond_force module#

molsysmt.thirds.openmm.forces.add_harmonic_bond_force.add_harmonic_bond_force(molecular_system=None, atom_pair=None, force_constant='1000 kilojoules_per_mole/nm**2', bond_length=None, pbc=False, return_force=False, syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.thirds.openmm.forces.add_plane_harmonic_restraint module#

molsysmt.thirds.openmm.forces.add_plane_harmonic_restraint.add_plane_harmonic_restraint(molecular_system=None, selection='all', force_constant='5000 kilojoules/(mol*nanometers**2)', point=None, normal_vector=[0, 0, 1], pbc=False, return_force=False, syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.thirds.openmm.forces.add_point_harmonic_restraint module#

molsysmt.thirds.openmm.forces.add_point_harmonic_restraint.add_point_harmonic_restraint(molecular_system, selection='all', force_constant='5000 kilojoules/(mol*nanometers**2)', point=None, pbc=False, return_force=False, syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.thirds.openmm.forces.pin_atoms module#

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

Module contents#