Add harmonic bond force#

Adding harmonic bond interaction potentials between specific atom pairs in OpenMM.

The function molsysmt.third_party.openmm.forces.add_harmonic_bond_force() adds a harmonic bond force between specified pairs of atom indices with custom equilibrium distances and spring constants.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects: molsysmt.third_party.openmm.forces.add_harmonic_bond_force().

Basic usage#

Let’s add harmonic bonds between atom pairs:

import molsysmt as msm

molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'], to_form='molsysmt.MolSys')
force = msm.third_party.openmm.forces.add_harmonic_bond_force(molsys, atom_pair=[[0, 10]], bond_length=['0.5 nm'], force_constant='1000 kJ/(mol*nm**2)', return_force=True)
print('Harmonic bond force created:', type(force))

Harmonic bond force created: <class 'openmm.openmm.HarmonicBondForce'>