ff.get_ordered_params(), complex_system, min_complex_coords)
# define NPT ensemble
potential_energy_model = PotentialEnergyModel(sys_params,
unbound_potentials)
ensemble = NPTEnsemble(potential_energy_model, temperature, pressure)
# define a thermostat
integrator = LangevinIntegrator(
temperature.value_in_unit(unit.kelvin),
timestep.value_in_unit(unit.picosecond),
collision_rate.value_in_unit(unit.picosecond**-1),
masses,
seed,
)
integrator_impl = integrator.impl()
def reduced_potential_fxn(x, box, lam):
u, du_dx = ensemble.reduced_potential_and_gradient(x, box, lam)
return u
# get list of molecules for barostat by looking at bond table
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
group_indices = get_group_indices(bond_list)
trajs = []
volume_trajs = []
# run at lambda=1.0, n_replicates times
lambdas = np.ones(n_replicates)
def test_barostat_partial_group_idxs():
"""Verify that the barostat can handle a subset of the molecules
rather than all of them. This test only verify that it runs, not the behavior"""
temperature = 300.0 * unit.kelvin
initial_waterbox_width = 3.0 * unit.nanometer
timestep = 1.5 * unit.femtosecond
barostat_interval = 3
collision_rate = 1.0 / unit.picosecond
seed = 2021
np.random.seed(seed)
pressure = 1.0 * unit.atmosphere
mol_a = hif2a_ligand_pair.mol_a
ff = hif2a_ligand_pair.ff
complex_system, complex_coords, complex_box, complex_top = build_water_system(
initial_waterbox_width.value_in_unit(unit.nanometer))
min_complex_coords = minimize_host_4d([mol_a], complex_system,
complex_coords, ff, complex_box)
afe = AbsoluteFreeEnergy(mol_a, ff)
unbound_potentials, sys_params, masses, coords = afe.prepare_host_edge(
ff.get_ordered_params(), complex_system, min_complex_coords)
# get list of molecules for barostat by looking at bond table
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
group_indices = get_group_indices(bond_list)
# Cut the number of groups in half
group_indices = group_indices[len(group_indices) // 2:]
lam = 1.0
bound_potentials = []
for params, unbound_pot in zip(sys_params, unbound_potentials):
bp = unbound_pot.bind(np.asarray(params))
bound_potentials.append(bp)
u_impls = []
for bp in bound_potentials:
bp_impl = bp.bound_impl(precision=np.float32)
u_impls.append(bp_impl)
integrator = LangevinIntegrator(
temperature.value_in_unit(unit.kelvin),
timestep.value_in_unit(unit.picosecond),
collision_rate.value_in_unit(unit.picosecond**-1),
masses,
seed,
)
integrator_impl = integrator.impl()
v_0 = sample_velocities(masses * unit.amu, temperature)
baro = custom_ops.MonteCarloBarostat(
coords.shape[0],
pressure.value_in_unit(unit.bar),
temperature.value_in_unit(unit.kelvin),
group_indices,
barostat_interval,
u_impls,
seed,
)
ctxt = custom_ops.Context(coords,
v_0,
complex_box,
integrator_impl,
u_impls,
barostat=baro)
ctxt.multiple_steps(np.ones(1000) * lam)
def test_barostat_varying_pressure():
temperature = 300.0 * unit.kelvin
initial_waterbox_width = 3.0 * unit.nanometer
timestep = 1.5 * unit.femtosecond
barostat_interval = 3
collision_rate = 1.0 / unit.picosecond
seed = 2021
np.random.seed(seed)
# Start out with a very large pressure
pressure = 1000.0 * unit.atmosphere
mol_a = hif2a_ligand_pair.mol_a
ff = hif2a_ligand_pair.ff
complex_system, complex_coords, complex_box, complex_top = build_water_system(
initial_waterbox_width.value_in_unit(unit.nanometer))
min_complex_coords = minimize_host_4d([mol_a], complex_system,
complex_coords, ff, complex_box)
afe = AbsoluteFreeEnergy(mol_a, ff)
unbound_potentials, sys_params, masses, coords = afe.prepare_host_edge(
ff.get_ordered_params(), complex_system, min_complex_coords)
# get list of molecules for barostat by looking at bond table
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
group_indices = get_group_indices(bond_list)
lam = 1.0
u_impls = []
for params, unbound_pot in zip(sys_params, unbound_potentials):
bp = unbound_pot.bind(np.asarray(params))
bp_impl = bp.bound_impl(precision=np.float32)
u_impls.append(bp_impl)
integrator = LangevinIntegrator(
temperature.value_in_unit(unit.kelvin),
timestep.value_in_unit(unit.picosecond),
collision_rate.value_in_unit(unit.picosecond**-1),
masses,
seed,
)
integrator_impl = integrator.impl()
v_0 = sample_velocities(masses * unit.amu, temperature)
baro = custom_ops.MonteCarloBarostat(
coords.shape[0],
pressure.value_in_unit(unit.bar),
temperature.value_in_unit(unit.kelvin),
group_indices,
barostat_interval,
u_impls,
seed,
)
ctxt = custom_ops.Context(coords,
v_0,
complex_box,
integrator_impl,
u_impls,
barostat=baro)
ctxt.multiple_steps(np.ones(1000) * lam)
ten_atm_box = ctxt.get_box()
ten_atm_box_vol = compute_box_volume(ten_atm_box)
# Expect the box to shrink thanks to the barostat
assert compute_box_volume(complex_box) - ten_atm_box_vol > 0.4
# Set the pressure to 1 bar
baro.set_pressure((1 * unit.atmosphere).value_in_unit(unit.bar))
# Changing the barostat interval resets the barostat step.
baro.set_interval(2)
ctxt.multiple_steps(np.ones(2000) * lam)
atm_box = ctxt.get_box()
# Box will grow thanks to the lower pressure
assert compute_box_volume(atm_box) > ten_atm_box_vol
def test_molecular_ideal_gas():
"""
References
----------
OpenMM testIdealGas
https://github.com/openmm/openmm/blob/d8ef57fed6554ec95684e53768188e1f666405c9/tests/TestMonteCarloBarostat.h#L86-L140
"""
# simulation parameters
initial_waterbox_width = 3.0 * unit.nanometer
timestep = 1.5 * unit.femtosecond
collision_rate = 1.0 / unit.picosecond
n_moves = 10000
barostat_interval = 5
seed = 2021
# thermodynamic parameters
temperatures = np.array([300, 600, 1000]) * unit.kelvin
pressure = 100.0 * unit.bar # very high pressure, to keep the expected volume small
# generate an alchemical system of a waterbox + alchemical ligand:
# effectively discard ligands by running in AbsoluteFreeEnergy mode at lambda = 1.0
mol_a = hif2a_ligand_pair.mol_a
ff = hif2a_ligand_pair.ff
complex_system, complex_coords, complex_box, complex_top = build_water_system(
initial_waterbox_width.value_in_unit(unit.nanometer))
min_complex_coords = minimize_host_4d([mol_a], complex_system,
complex_coords, ff, complex_box)
afe = AbsoluteFreeEnergy(mol_a, ff)
_unbound_potentials, _sys_params, masses, coords = afe.prepare_host_edge(
ff.get_ordered_params(), complex_system, min_complex_coords)
# drop the nonbonded potential
unbound_potentials = _unbound_potentials[:-1]
sys_params = _sys_params[:-1]
# get list of molecules for barostat by looking at bond table
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
group_indices = get_group_indices(bond_list)
volume_trajs = []
relative_tolerance = 1e-2
initial_relative_box_perturbation = 2 * relative_tolerance
n_molecules = complex_top.getNumResidues()
bound_potentials = []
for params, unbound_pot in zip(sys_params, unbound_potentials):
bp = unbound_pot.bind(np.asarray(params))
bound_potentials.append(bp)
u_impls = []
for bp in bound_potentials:
bp_impl = bp.bound_impl(precision=np.float32)
u_impls.append(bp_impl)
# expected volume
md_pressure_unit = ENERGY_UNIT / DISTANCE_UNIT**3
pressure_in_md = (
pressure * unit.AVOGADRO_CONSTANT_NA).value_in_unit(md_pressure_unit)
expected_volume_in_md = (n_molecules +
1) * BOLTZ * temperatures.value_in_unit(
unit.kelvin) / pressure_in_md
for i, temperature in enumerate(temperatures):
# define a thermostat
integrator = LangevinIntegrator(
temperature.value_in_unit(unit.kelvin),
timestep.value_in_unit(unit.picosecond),
collision_rate.value_in_unit(unit.picosecond**-1),
masses,
seed,
)
integrator_impl = integrator.impl()
v_0 = sample_velocities(masses * unit.amu, temperature)
# rescale the box to be approximately the desired box volume already
rescaler = CentroidRescaler(group_indices)
initial_volume = compute_box_volume(complex_box)
initial_center = compute_box_center(complex_box)
length_scale = ((1 + initial_relative_box_perturbation) *
expected_volume_in_md[i] / initial_volume)**(1.0 / 3)
new_coords = rescaler.scale_centroids(coords, initial_center,
length_scale)
new_box = complex_box * length_scale
baro = custom_ops.MonteCarloBarostat(
new_coords.shape[0],
pressure.value_in_unit(unit.bar),
temperature.value_in_unit(unit.kelvin),
group_indices,
barostat_interval,
u_impls,
seed,
)
ctxt = custom_ops.Context(new_coords,
v_0,
new_box,
integrator_impl,
u_impls,
barostat=baro)
vols = []
for move in range(n_moves // barostat_interval):
ctxt.multiple_steps(np.ones(barostat_interval))
new_box = ctxt.get_box()
volume = np.linalg.det(new_box)
vols.append(volume)
volume_trajs.append(vols)
equil_time = len(volume_trajs[0]) // 2 # TODO: don't hard-code this?
actual_volume_in_md = np.array(
[np.mean(volume_traj[equil_time:]) for volume_traj in volume_trajs])
np.testing.assert_allclose(actual=actual_volume_in_md,
desired=expected_volume_in_md,
rtol=relative_tolerance)
def test_barostat_is_deterministic():
"""Verify that the barostat results in the same box size shift after 1000
steps. This is important to debugging as well as providing the ability to replicate
simulations
"""
platform_version = get_platform_version()
lam = 1.0
temperature = 300.0 * unit.kelvin
initial_waterbox_width = 3.0 * unit.nanometer
timestep = 1.5 * unit.femtosecond
barostat_interval = 3
collision_rate = 1.0 / unit.picosecond
seed = 2021
np.random.seed(seed)
# OpenEye's AM1 Charging values are OS platform dependent. To ensure that we have deterministic values
# we check against our two most common OS versions, Ubuntu 18.04 and 20.04.
box_vol = 26.869380588831582
lig_charge_vals = np.array([
1.4572377542719206, -0.37011462071257184, 1.1478267014520305,
-4.920284514559682, 0.16985194917937935
])
if "ubuntu" not in platform_version:
print(
f"Test expected to run under ubuntu 20.04 or 18.04, got {platform_version}"
)
if "18.04" in platform_version:
box_vol = 26.711716908713402
lig_charge_vals[3] = -4.920166483601927
pressure = 1.0 * unit.atmosphere
mol_a = hif2a_ligand_pair.mol_a
ff = hif2a_ligand_pair.ff
complex_system, complex_coords, complex_box, complex_top = build_water_system(
initial_waterbox_width.value_in_unit(unit.nanometer))
min_complex_coords = minimize_host_4d([mol_a], complex_system,
complex_coords, ff, complex_box)
afe = AbsoluteFreeEnergy(mol_a, ff)
unbound_potentials, sys_params, masses, coords = afe.prepare_host_edge(
ff.get_ordered_params(), complex_system, min_complex_coords)
# get list of molecules for barostat by looking at bond table
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
group_indices = get_group_indices(bond_list)
u_impls = []
# Look at the first five atoms and their assigned charges
ligand_charges = sys_params[-1][:, 0][len(min_complex_coords):][:5]
np.testing.assert_array_almost_equal(lig_charge_vals,
ligand_charges,
decimal=5)
for params, unbound_pot in zip(sys_params, unbound_potentials):
bp = unbound_pot.bind(np.asarray(params))
bp_impl = bp.bound_impl(precision=np.float32)
u_impls.append(bp_impl)
integrator = LangevinIntegrator(
temperature.value_in_unit(unit.kelvin),
timestep.value_in_unit(unit.picosecond),
collision_rate.value_in_unit(unit.picosecond**-1),
masses,
seed,
)
integrator_impl = integrator.impl()
v_0 = sample_velocities(masses * unit.amu, temperature)
baro = custom_ops.MonteCarloBarostat(
coords.shape[0],
pressure.value_in_unit(unit.bar),
temperature.value_in_unit(unit.kelvin),
group_indices,
barostat_interval,
u_impls,
seed,
)
ctxt = custom_ops.Context(coords,
v_0,
complex_box,
integrator_impl,
u_impls,
barostat=baro)
ctxt.multiple_steps(np.ones(1000) * lam)
atm_box = ctxt.get_box()
np.testing.assert_almost_equal(compute_box_volume(atm_box),
box_vol,
decimal=5)