def test_cutoff_electrostatics():
ion_ff = ForceField(get_test_file_path("ions.offxml"))
ions = Topology.from_molecules([
Molecule.from_smiles("[#3]"),
Molecule.from_smiles("[#17]"),
])
out = Interchange.from_smirnoff(ion_ff, ions)
out.box = [4, 4, 4] * unit.nanometer
gmx = []
lmp = []
for d in np.linspace(0.75, 0.95, 5):
positions = np.zeros((2, 3)) * unit.nanometer
positions[1, 0] = d * unit.nanometer
out.positions = positions
out["Electrostatics"].method = "cutoff"
gmx.append(
get_gromacs_energies(out, mdp="auto").energies["Electrostatics"].m)
lmp.append(
get_lammps_energies(out).energies["Electrostatics"].m_as(
unit.kilojoule / unit.mol))
assert np.sum(np.sqrt(np.square(np.asarray(lmp) - np.asarray(gmx)))) < 1e-3
def _get_mdp_file(key: str = "auto") -> str:
if key == "auto":
return "auto_generated.mdp"
mapping = {
"default": "default.mdp",
"cutoff": "cutoff.mdp",
"cutoff_hbonds": "cutoff_hbonds.mdp",
"cutoff_buck": "cutoff_buck.mdp",
}
return get_test_file_path(f"mdp/{mapping[key]}")
def test_liquid_argon():
argon = Molecule.from_smiles("[#18]")
pdbfile = app.PDBFile(get_test_file_path("packed-argon.pdb"))
top = Topology.from_openmm(pdbfile.topology, unique_molecules=[argon])
argon_ff = ForceField(get_test_file_path("argon.offxml"))
out = Interchange.from_smirnoff(argon_ff, top)
out.positions = pdbfile.positions
omm_energies = get_openmm_energies(out)
gmx_energies = get_gromacs_energies(
out,
mdp="auto",
writer="internal",
)
omm_energies.compare(
gmx_energies,
custom_tolerances={
"vdW": 0.008 * simtk_unit.kilojoule_per_mole,
},
)
argon_ff_no_switch = deepcopy(argon_ff)
argon_ff_no_switch["vdW"].switch_width *= 0
out_no_switch = Interchange.from_smirnoff(argon_ff_no_switch, top)
out_no_switch.positions = pdbfile.positions
lmp_energies = get_lammps_energies(out_no_switch)
omm_energies.compare(
lmp_energies,
custom_tolerances={
"vdW": 10.5 * simtk_unit.kilojoule_per_mole,
},
)
def test_water_dimer():
tip3p = ForceField(get_test_file_path("tip3p.offxml"))
water = Molecule.from_smiles("O")
top = Topology.from_molecules(2 * [water])
top.mdtop = md.Topology.from_openmm(top.to_openmm())
pdbfile = openmm.app.PDBFile(get_test_file_path("water-dimer.pdb"))
positions = pdbfile.positions
openff_sys = Interchange.from_smirnoff(tip3p, top)
openff_sys.positions = positions
openff_sys.box = [10, 10, 10] * unit.nanometer
omm_energies = get_openmm_energies(
openff_sys,
hard_cutoff=True,
electrostatics=False,
)
toolkit_energies = _get_openmm_energies(
tip3p.create_openmm_system(top),
openff_sys.box,
openff_sys.positions,
hard_cutoff=True,
electrostatics=False,
)
omm_energies.compare(toolkit_energies)
# TODO: Fix GROMACS energies by handling SETTLE constraints
# gmx_energies, _ = get_gromacs_energies(openff_sys)
# compare_gromacs_openmm(omm_energies=omm_energies, gmx_energies=gmx_energies)
openff_sys["Electrostatics"].method = "cutoff"
omm_energies_cutoff = get_gromacs_energies(openff_sys)
lmp_energies = get_lammps_energies(openff_sys)
lmp_energies.compare(omm_energies_cutoff)
def ammonia_ff(self):
"""Fixture that loads an SMIRNOFF XML for ammonia"""
return ForceField(get_test_file_path("ammonia.offxml"))
def argon_ff(self):
"""Fixture that loads an SMIRNOFF XML for argon"""
return ForceField(get_test_file_path("argon.offxml"))
_compare_nonbonded_parameters(
_get_force(toolkit_sys, openmm.NonbondedForce),
_get_force(new_sys, openmm.NonbondedForce),
)
if "Bond" in str(e):
raise e
if "Angle" in str(e):
raise e
@skip_if_missing("openff.evaluator")
@pytest.mark.timeout(60)
@pytest.mark.slow()
@pytest.mark.parametrize(
"rdmol",
Chem.SDMolSupplier(get_test_file_path("MiniDrugBankTrimmed.sdf"), sanitize=False),
)
def test_energy_vs_toolkit(rdmol):
Chem.SanitizeMol(rdmol)
mol = Molecule.from_rdkit(rdmol, allow_undefined_stereo=True)
mol.to_inchi()
assert mol.n_conformers > 0
max_n_heavy_atoms = 12
if len([a for a in mol.atoms if a.atomic_number > 1]) > max_n_heavy_atoms:
pytest.skip(f"Skipping > {max_n_heavy_atoms} heavy atoms for now")
# Skip molecules that cause hangs due to the toolkit taking an excessive time