def test_load_prmtop(self):
struct = readparm.LoadParm(get_pmd_fn("trx.prmtop"))
other_struct = readparm.AmberParm(get_pmd_fn("trx.prmtop"))
prmtop = Interchange._from_parmed(struct)
other_prmtop = Interchange._from_parmed(other_struct)
for handler_key in prmtop.handlers:
# TODO: Closer inspection of data
assert handler_key in other_prmtop.handlers
assert not prmtop.box
struct.box = [20, 20, 20, 90, 90, 90]
prmtop_converted = Interchange._from_parmed(struct)
np.testing.assert_allclose(prmtop_converted.box,
np.eye(3) * 2.0 * unit.nanometer)
def test_read_box_parm7(self):
top = readparm.LoadParm(get_pmd_fn("solv2.parm7"))
out = Interchange._from_parmed(top)
# pmd.load_file(get_pmd_fn("solv2.rst7")))
# top = readparm.LoadParm(get_pmd_fn("solv2.parm7"), xyz=coords.coordinates)
np.testing.assert_allclose(np.diag(out.box.m_as(unit.angstrom)),
top.parm_data["BOX_DIMENSIONS"][1:])
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,
},
)