openff-interchange documentation

Energy Tests

This project includes infrastructure for comparing representations of parametrized systems via computing single-point energies using molecular simulation engines.

Currently, OpenMM, GROMACS, and LAMMPS are supported engines for running energy tests. There are high-level functions for computing energies from constructed System objects. There are also some internal functions that can be used to compute energies from other inputs.

This example shows many ways of computing single-point energies from a constructed System object.

import numpy as np

# Create an OpenFF System object from an OpenFF Molecule, Topology, and ForceField
from openff.toolkit.topology import Molecule
from openff.system.stubs import ForceField

molecule = Molecule.from_smiles("CCO")
molecule.generate_conformers(n_conformers=1)
topology = molecule.to_topology()
forcefield = ForceField("openff-1.2.0.offxml")
openff_system = forcefield.create_openff_system(topology)
openff_system.box = [5, 5, 5]
openff_system.positions = np.round(molecule.conformers[0]._value / 10.0, 3)


# Directly compute single-point energies via OpenMM, GROMACS, and LAMMPS
from openff.system.tests.energy_tests.openmm import get_openmm_energies
from openff.system.tests.energy_tests.gromacs import get_gromacs_energies
from openff.system.tests.energy_tests.lammps import get_lammps_energies

openmm_energies = get_openmm_energies(openff_system)
gmx_energies = get_gromacs_energies(openff_system)
lmp_energies = get_lammps_energies(openff_system)

# Compare energies computed from different engines
openmm_energies.compare(gmx_energies)  # EnergyError: ...
gmx_energies.compare(lmp_energies)  # EnergyError: ...


# Compute single-point energies from engine-specific files/objects
from openff.system.tests.energy_tests.openmm import _get_openmm_energies

_get_openmm_energies(
    omm_sys=openff_system.to_openmm(),
    box_vectors=openff_system.box,
    positions=openff_system.positions,
)

from openff_system.tests.energy_tests.gromacs import _run_gmx_energy, _get_mdp_file

openff_sys.to_top("out.top", writer="internal")
openff_sys.to_gro("out.gro", writer="internal")

_run_gmx_energy(
    top_file="out.top",
    gro_file="out.gro",
    mdp_file=_get_mdp_file("cutoff_hbonds"),
)