def test_rb_torsions_vs_foyer(self, ethanol_with_rb_torsions):
# Given that these force constants are copied from Foyer's OPLS-AA file,
# compare to processing through the current MoSDeF pipeline
import foyer
import mbuild
comp = mbuild.load("CC", smiles=True)
comp.xyz = ethanol_with_rb_torsions.positions.m_as(unit.nanometer)
ff = foyer.Forcefield(name="oplsaa")
from_foyer = ff.apply(comp)
from_foyer.box = [40, 40, 40, 90, 90, 90]
from_foyer.save("from_foyer.top")
from_foyer.save("from_foyer.gro")
rb_torsion_energy_from_foyer = _run_gmx_energy(
top_file="from_foyer.top",
gro_file="from_foyer.gro",
mdp_file=_get_mdp_file("default"),
).energies["Torsion"]
# GROMACS vs. OpenMM was already compared, so just use one
omm = get_gromacs_energies(ethanol_with_rb_torsions, decimal=3).energies[
"Torsion"
]
assert (omm - rb_torsion_energy_from_foyer).m_as(kj_mol) < 1e-6
def test_interchange_energies(self, molecule_path, get_interchanges, oplsaa):
if "ethanol" in molecule_path or "adamantane" in molecule_path:
pytest.skip("Foyer/ParmEd bug with this molecule")
openff_interchange, pmd_structure = get_interchanges(molecule_path)
parameterized_pmd_structure = oplsaa.apply(pmd_structure)
openff_energy = get_gromacs_energies(
openff_interchange, decimal=3, mdp="cutoff_hbonds"
)
parameterized_pmd_structure.save("from_foyer.gro")
parameterized_pmd_structure.save("from_foyer.top")
through_foyer = _run_gmx_energy(
top_file="from_foyer.top",
gro_file="from_foyer.gro",
mdp_file=_get_mdp_file("cutoff_hbonds"),
)
# TODO: Revisit after https://github.com/mosdef-hub/foyer/issues/431
openff_energy.compare(
through_foyer,
custom_tolerances={
"Bond": 1e-3 * unit.kilojoule / unit.mole,
"Angle": 1e-3 * unit.kilojoule / unit.mole,
"Nonbonded": 1e-3 * unit.kilojoule / unit.mole,
"Torsion": 1e-3 * unit.kilojoule / unit.mole,
"vdW": 5 * unit.kilojoule / unit.mole,
"Electrostatics": 1 * unit.kilojoule / unit.mole,
},
)
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 test_rb_torsions(self, ethanol_with_rb_torsions):
omm = get_openmm_energies(ethanol_with_rb_torsions, round_positions=3).energies[
"Torsion"
]
gmx = get_gromacs_energies(ethanol_with_rb_torsions, decimal=3).energies[
"Torsion"
]
assert (gmx - omm).m_as(kj_mol) < 1e-6
def test_parmed_roundtrip(self):
original = pmd.load_file(get_test_file_path("ALA_GLY/ALA_GLY.top"))
gro = pmd.load_file(get_test_file_path("ALA_GLY/ALA_GLY.gro"))
original.box = gro.box
original.positions = gro.positions
openff_sys = Interchange._from_parmed(original)
openff_sys.topology.mdtop = md.Topology.from_openmm(gro.topology)
# Some sanity checks, including that residues are stored ...
assert openff_sys.topology.mdtop.n_atoms == 29
# TODO: Assert number of topology molecules after refactor
assert openff_sys.topology.mdtop.n_residues == 4
# ... and written out
openff_sys.to_gro("has_residues.gro", writer="internal")
assert len(pmd.load_file("has_residues.gro").residues) == 4
roundtrip = openff_sys._to_parmed()
roundtrip.save("conv.gro", overwrite=True)
roundtrip.save("conv.top", overwrite=True)
original_energy = _run_gmx_energy(
top_file=get_test_file_path("ALA_GLY/ALA_GLY.top"),
gro_file=get_test_file_path("ALA_GLY/ALA_GLY.gro"),
mdp_file=_get_mdp_file("cutoff_hbonds"),
)
internal_energy = get_gromacs_energies(openff_sys, mdp="cutoff_hbonds")
roundtrip_energy = _run_gmx_energy(
top_file="conv.top",
gro_file="conv.gro",
mdp_file=_get_mdp_file("cutoff_hbonds"),
)
# Differences in bond energies appear to be related to ParmEd's rounding
# of the force constant and equilibrium bond length
original_energy.compare(internal_energy)
internal_energy.compare(
roundtrip_energy,
custom_tolerances={
"Bond": 0.02 * omm_unit.kilojoule_per_mole,
},
)
original_energy.compare(
roundtrip_energy,
custom_tolerances={
"Bond": 0.02 * omm_unit.kilojoule_per_mole,
},
)
def test_ethanol_energies(self, oplsaa_interchange_ethanol):
from openff.interchange.tests.energy_tests.test_energies import (
get_gromacs_energies,
)
gmx_energies = get_gromacs_energies(oplsaa_interchange_ethanol)
omm_energies = get_openmm_energies(oplsaa_interchange_ethanol)
gmx_energies.compare(
omm_energies,
custom_tolerances={
"vdW": 12.0 * unit.kilojoule / unit.mole,
"Electrostatics": 12.0 * unit.kilojoule / unit.mole,
},
)
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 test_gmx_14_energies_exist():
# TODO: Make sure 1-4 energies are accurate, not just existent
# Use a molecule with only one 1-4 interaction, and
# make it between heavy atoms because H-H 1-4 are weak
mol = Molecule.from_smiles("ClC#CCl")
mol.name = "HPER"
mol.generate_conformers(n_conformers=1)
parsley = ForceField("openff-1.0.0.offxml")
out = Interchange.from_smirnoff(parsley, mol.to_topology())
out.positions = mol.conformers[0]
# Put this molecule in a large box with cut-off electrostatics
# to prevent it from interacting with images of itself
out.box = [40, 40, 40]
out["Electrostatics"].method = "cutoff"
gmx_energies = get_gromacs_energies(out)
# The only possible non-bonded interactions should be from 1-4 intramolecular interactions
assert gmx_energies.energies["vdW"].m != 0.0
assert gmx_energies.energies["Electrostatics"].m != 0.0
def test_energies_single_mol(constrained, mol_smi):
import mbuild as mb
mol = Molecule.from_smiles(mol_smi)
mol.generate_conformers(n_conformers=1)
mol.name = "FOO"
top = mol.to_topology()
top.box_vectors = None # [10, 10, 10] * simtk_unit.nanometer
if constrained:
parsley = ForceField("openff-1.0.0.offxml")
else:
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
off_sys = Interchange.from_smirnoff(parsley, top)
off_sys.handlers["Electrostatics"].method = "cutoff"
mol.to_file("out.xyz", file_format="xyz")
compound: mb.Compound = mb.load("out.xyz")
packed_box: mb.Compound = mb.fill_box(compound=compound,
n_compounds=1,
box=mb.Box(lengths=[10, 10, 10]))
positions = packed_box.xyz * unit.nanometer
off_sys.positions = positions
# Compare directly to toolkit's reference implementation
omm_energies = get_openmm_energies(off_sys, round_positions=8)
omm_reference = parsley.create_openmm_system(top)
reference_energies = _get_openmm_energies(
omm_sys=omm_reference,
box_vectors=off_sys.box,
positions=off_sys.positions,
round_positions=8,
)
omm_energies.compare(reference_energies)
mdp = "cutoff_hbonds" if constrained else "auto"
# Compare GROMACS writer and OpenMM export
gmx_energies = get_gromacs_energies(off_sys, mdp=mdp)
custom_tolerances = {
"Bond": 2e-5 * simtk_unit.kilojoule_per_mole,
"Electrostatics": 2 * simtk_unit.kilojoule_per_mole,
"vdW": 2 * simtk_unit.kilojoule_per_mole,
"Nonbonded": 2 * simtk_unit.kilojoule_per_mole,
"Angle": 1e-4 * simtk_unit.kilojoule_per_mole,
}
gmx_energies.compare(
omm_energies,
custom_tolerances=custom_tolerances,
)
if not constrained:
other_energies = get_openmm_energies(
off_sys,
round_positions=8,
hard_cutoff=True,
electrostatics=True,
)
lmp_energies = get_lammps_energies(off_sys)
custom_tolerances = {
"vdW": 5.0 * simtk_unit.kilojoule_per_mole,
"Electrostatics": 5.0 * simtk_unit.kilojoule_per_mole,
}
lmp_energies.compare(other_energies,
custom_tolerances=custom_tolerances)
def test_packmol_boxes(toolkit_file_path):
# TODO: Isolate a set of systems here instead of using toolkit data
# TODO: Fix nonbonded energy differences
from openff.toolkit.utils import get_data_file_path
pdb_file_path = get_data_file_path(toolkit_file_path)
pdbfile = openmm.app.PDBFile(pdb_file_path)
ethanol = Molecule.from_smiles("CCO")
cyclohexane = Molecule.from_smiles("C1CCCCC1")
omm_topology = pdbfile.topology
off_topology = OFFBioTop.from_openmm(
omm_topology, unique_molecules=[ethanol, cyclohexane])
off_topology.mdtop = md.Topology.from_openmm(omm_topology)
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
off_sys = Interchange.from_smirnoff(parsley, off_topology)
off_sys.box = np.asarray(
pdbfile.topology.getPeriodicBoxVectors().value_in_unit(
simtk_unit.nanometer))
off_sys.positions = pdbfile.positions
sys_from_toolkit = parsley.create_openmm_system(off_topology)
omm_energies = get_openmm_energies(off_sys,
hard_cutoff=True,
electrostatics=False)
reference = _get_openmm_energies(
sys_from_toolkit,
off_sys.box,
off_sys.positions,
hard_cutoff=True,
electrostatics=False,
)
omm_energies.compare(
reference,
custom_tolerances={
"Electrostatics": 2e-2 * simtk_unit.kilojoule_per_mole,
},
)
# custom_tolerances={"HarmonicBondForce": 1.0}
# Compare GROMACS writer and OpenMM export
gmx_energies = get_gromacs_energies(off_sys, electrostatics=False)
omm_energies_rounded = get_openmm_energies(
off_sys,
round_positions=8,
hard_cutoff=True,
electrostatics=False,
)
omm_energies_rounded.compare(
other=gmx_energies,
custom_tolerances={
"Angle": 1e-2 * simtk_unit.kilojoule_per_mole,
"Torsion": 1e-2 * simtk_unit.kilojoule_per_mole,
"Electrostatics": 3200 * simtk_unit.kilojoule_per_mole,
},
)