def test_bigger_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(
self.mock_parm,
solvation_type="explicit",
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=True,
implicit_solvent="vacuum",
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.PME,
nonbondedCutoff=1.0,
constraints=ff.AllBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=4.0 * gram / mole,
ewaldErrorTolerance=self.pme_params.tolerance,
)
def test_cutoff_sets_correct_method(self):
_create_openmm_system(
self.mock_parm,
solvation_type="implicit",
cutoff=1.5,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent="obc",
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False,
nonbondedMethod=ff.CutoffNonPeriodic,
nonbondedCutoff=1.5,
constraints=ff.HBonds,
implicitSolvent=OBC2,
hydrogenMass=None,
implicitSolventSaltConc=0.0,
soluteDielectric=1.0,
solventDielectric=78.5,
)
def test_big_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(
self.mock_parm,
solvation_type="implicit",
cutoff=None,
use_big_timestep=True,
use_bigger_timestep=False,
implicit_solvent="obc",
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False,
nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=999.,
constraints=ff.AllBonds,
implicitSolvent=OBC2,
hydrogenMass=3.0 * (gram / mole),
implicitSolventSaltConc=0.0,
soluteDielectric=1.0,
solventDielectric=78.5,
)
def test_pressure_coupling_should_add_barostat(self):
PRESS = 2.0 * atmosphere
STEPS = 50
pcouple_params = PressureCouplingParams(
enable=True,
temperature=self.TEMP,
pressure=PRESS,
steps=STEPS)
pme_params = PMEParams(
enable=True,
tolerance=0.0005)
with mock.patch('meld.system.openmm_runner.runner.MonteCarloBarostat',
spec=MonteCarloBarostat) as mock_baro:
mock_baro.return_value = mock.sentinel.baro_force
_create_openmm_system(
self.mock_parm,
solvation_type='explicit',
cutoff=1.0,
use_big_timestep=False, use_bigger_timestep=False,
implicit_solvent='vacuum',
pme_params=pme_params,
pcouple_params=pcouple_params,
remove_com=True,
temperature=self.TEMP)
mock_baro.assert_called_with(PRESS, self.TEMP, STEPS)
mock_sys = self.mock_parm.createSystem.return_value
mock_sys.addForce.assert_called_with(mock.sentinel.baro_force)
def test_no_pme_uses_cutoffs(self):
pme_params = PMEParams(enable=False, tolerance=0.0001)
_create_openmm_system(
self.mock_parm,
solvation_type="explicit",
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent="vacuum",
pme_params=pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.CutoffPeriodic,
nonbondedCutoff=1.0,
constraints=ff.HBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=None,
ewaldErrorTolerance=pme_params.tolerance,
)
def test_cutoff_sets_correct_method(self):
_create_openmm_system(
self.mock_parm,
solvation_type="implicit",
cutoff=1.5,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent="obc",
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False,
nonbondedMethod=ff.CutoffNonPeriodic,
nonbondedCutoff=1.5,
constraints=ff.HBonds,
implicitSolvent=OBC2,
hydrogenMass=None,
implicitSolventSaltConc=0.0,
soluteDielectric=1.0,
solventDielectric=78.5,
)
def test_bigger_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(
self.mock_parm,
solvation_type="explicit",
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=True,
implicit_solvent="vacuum",
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.PME,
nonbondedCutoff=1.0,
constraints=ff.AllBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=4.0 * gram / mole,
ewaldErrorTolerance=self.pme_params.tolerance,
)
def test_no_pme_uses_cutoffs(self):
pme_params = PMEParams(enable=False, tolerance=0.0001)
_create_openmm_system(
self.mock_parm,
solvation_type="explicit",
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent="vacuum",
pme_params=pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.CutoffPeriodic,
nonbondedCutoff=1.0,
constraints=ff.HBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=None,
ewaldErrorTolerance=pme_params.tolerance,
)
def test_big_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(
self.mock_parm,
solvation_type="implicit",
cutoff=None,
use_big_timestep=True,
use_bigger_timestep=False,
implicit_solvent="obc",
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False,
nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=999.,
constraints=ff.AllBonds,
implicitSolvent=OBC2,
hydrogenMass=3.0 * (gram / mole),
implicitSolventSaltConc=0.0,
soluteDielectric=1.0,
solventDielectric=78.5,
)
def test_no_cutoff_should_set_correct_method(self):
_create_openmm_system(
self.mock_parm,
solvation_type='implicit',
cutoff=None, use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent='obc',
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=999.,
constraints=ff.HBonds, implicitSolvent=OBC2, hydrogenMass=None)
def test_big_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(
self.mock_parm,
solvation_type='implicit',
cutoff=None,
use_big_timestep=True, use_bigger_timestep=False,
implicit_solvent='obc',
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False, nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=999., constraints=ff.AllBonds,
implicitSolvent=OBC2, hydrogenMass=3.0 * (gram / mole))
def test_bigger_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(
self.mock_parm,
solvation_type='explicit',
cutoff=1.0,
use_big_timestep=False, use_bigger_timestep=True,
implicit_solvent='vacuum',
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.PME,
nonbondedCutoff=1.0,
constraints=ff.AllBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=4.0 * gram / mole,
ewaldErrorTolerance=self.pme_params.tolerance)
def test_gbneck2_sets_correct_solvent_model(self):
_create_openmm_system(self.mock_parm,
solvation_type='implicit',
cutoff=None,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent='gbNeck2',
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=False,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[])
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=False,
nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=999.,
constraints=ff.HBonds,
implicitSolvent=GBn2,
hydrogenMass=None)
def test_enables_pme_and_cutoffs(self):
_create_openmm_system(self.mock_parm,
solvation_type='explicit',
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent='vacuum',
pme_params=self.pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[])
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.PME,
nonbondedCutoff=1.0,
constraints=ff.HBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=None,
ewaldErrorTolerance=self.pme_params.tolerance)
def test_pressure_coupling_should_add_barostat(self):
PRESS = 2.0 * atmosphere
STEPS = 50
pcouple_params = PressureCouplingParams(enable=True,
temperature=self.TEMP,
pressure=PRESS,
steps=STEPS)
pme_params = PMEParams(enable=True, tolerance=0.0005)
with mock.patch(
"meld.system.openmm_runner.runner.MonteCarloBarostat",
spec=MonteCarloBarostat,
) as mock_baro:
mock_baro.return_value = mock.sentinel.baro_force
_create_openmm_system(
self.mock_parm,
solvation_type="explicit",
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent="vacuum",
pme_params=pme_params,
pcouple_params=pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
mock_baro.assert_called_with(PRESS, self.TEMP, STEPS)
mock_sys = self.mock_parm.createSystem.return_value
mock_sys.addForce.assert_called_with(mock.sentinel.baro_force)
def test_no_pme_uses_cutoffs(self):
pme_params = PMEParams(
enable=False,
tolerance=0.0001)
_create_openmm_system(
self.mock_parm,
solvation_type='explicit',
cutoff=1.0,
use_big_timestep=False, use_bigger_timestep=False,
implicit_solvent='vacuum',
pme_params=pme_params,
pcouple_params=self.pcouple_params,
remove_com=True,
temperature=self.TEMP)
self.mock_parm.createSystem.assert_called_with(
removeCMMotion=True,
nonbondedMethod=ff.CutoffPeriodic,
nonbondedCutoff=1.0,
constraints=ff.HBonds,
implicitSolvent=None,
rigidWater=True,
hydrogenMass=None,
ewaldErrorTolerance=pme_params.tolerance)
def test_pressure_coupling_should_add_barostat(self):
PRESS = 2.0 * atmosphere
STEPS = 50
pcouple_params = PressureCouplingParams(
enable=True, temperature=self.TEMP, pressure=PRESS, steps=STEPS
)
pme_params = PMEParams(enable=True, tolerance=0.0005)
with mock.patch(
"meld.system.openmm_runner.runner.MonteCarloBarostat",
spec=MonteCarloBarostat,
) as mock_baro:
mock_baro.return_value = mock.sentinel.baro_force
_create_openmm_system(
self.mock_parm,
solvation_type="explicit",
cutoff=1.0,
use_big_timestep=False,
use_bigger_timestep=False,
implicit_solvent="vacuum",
pme_params=pme_params,
pcouple_params=pcouple_params,
remove_com=True,
temperature=self.TEMP,
extra_bonds=[],
extra_restricted_angles=[],
extra_torsions=[],
implicitSolventSaltConc=None,
soluteDielectric=None,
solventDielectric=None,
)
mock_baro.assert_called_with(PRESS, self.TEMP, STEPS)
mock_sys = self.mock_parm.createSystem.return_value
mock_sys.addForce.assert_called_with(mock.sentinel.baro_force)
def test_big_timestep_sets_allbonds_and_hydrogen_masses(self):
_create_openmm_system(self.mock_parm, cutoff=None, use_big_timestep=True, implicit_solvent='obc', remove_com=False)
self.mock_parm.createSystem.assert_called_with(removeCMMotion=False, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=999.,
constraints=ff.AllBonds, implicitSolvent=OBC2, hydrogenMass=3.0 * (gram / mole))
def test_cutoff_sets_correct_method(self):
_create_openmm_system(self.mock_parm, cutoff=1.5, use_big_timestep=False, implicit_solvent='obc', remove_com=False)
self.mock_parm.createSystem.assert_called_with(removeCMMotion=False, nonbondedMethod=ff.CutoffNonPeriodic, nonbondedCutoff=1.5,
constraints=ff.HBonds, implicitSolvent=OBC2, hydrogenMass=None)
def test_gbneck2_sets_correct_solvent_model(self):
_create_openmm_system(self.mock_parm, cutoff=None, use_big_timestep=False, implicit_solvent='gbNeck2', remove_com=False)
self.mock_parm.createSystem.assert_called_with(removeCMMotion=False, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=999.,
constraints=ff.HBonds, implicitSolvent=GBn2, hydrogenMass=None)
