def vacuum_model(ff_params):
unbound_potentials, sys_params, masses, coords = rfe.prepare_vacuum_edge(
ff_params)
x0 = coords
v0 = np.zeros_like(coords)
client = CUDAPoolClient(1)
box = np.eye(3, dtype=np.float64) * 100
harmonic_bond_potential = unbound_potentials[0]
group_idxs = get_group_indices(get_bond_list(harmonic_bond_potential))
x0 = coords
v0 = np.zeros_like(coords)
client = CUDAPoolClient(1)
temperature = 300.0
pressure = 1.0
integrator = LangevinIntegrator(temperature, 1.5e-3, 1.0, masses, seed)
barostat = MonteCarloBarostat(x0.shape[0], pressure, temperature,
group_idxs, 25, seed)
model = estimator.FreeEnergyModel(unbound_potentials, client, box, x0,
v0, integrator, lambda_schedule,
equil_steps, prod_steps, barostat)
return estimator.deltaG(model, sys_params)[0]
def test_free_energy_estimator():
n_atoms = 5
x0 = np.random.rand(n_atoms, 3)
v0 = np.zeros_like(x0)
n_bonds = 3
n_angles = 4
hb_pot, hb_params = get_harmonic_bond(n_atoms, n_bonds)
ha_pot, ha_params = get_harmonic_angle(n_atoms, n_angles)
sys_params = [hb_params, ha_params]
unbound_potentials = [hb_pot, ha_pot]
masses = np.random.rand(n_atoms)
box = np.eye(3, dtype=np.float64)
seed = 2021
group_idxs = get_group_indices(get_bond_list(hb_pot))
temperature = 300.0
pressure = 1.0
integrator = LangevinIntegrator(temperature, 1.5e-3, 1.0, masses, seed)
barostat = MonteCarloBarostat(x0.shape[0], pressure, temperature,
group_idxs, 25, seed)
beta = 0.125
lambda_schedule = np.linspace(0, 1.0, 4)
def loss_fn(sys_params):
endpoint_correct = False
mdl = estimator_abfe.FreeEnergyModel(
unbound_potentials,
endpoint_correct,
client,
box,
x0,
v0,
integrator,
barostat,
lambda_schedule,
100,
100,
beta,
"test",
)
dG, bar_dG_err, results = estimator_abfe.deltaG(mdl, sys_params)
return dG**2
for client in [None, CUDAPoolClient(1)]:
loss_fn(sys_params)
def __init__(
self,
ubps,
lamb,
masses,
temperature,
pressure,
n_steps,
seed,
dt=1.5e-3,
friction=1.0,
barostat_interval=5,
):
intg = lib.LangevinIntegrator(temperature, dt, friction, masses, seed)
self.integrator_impl = intg.impl()
all_impls = [bp.bound_impl(np.float32) for bp in ubps]
bond_list = get_bond_list(ubps[0])
group_idxs = get_group_indices(bond_list)
barostat = lib.MonteCarloBarostat(len(masses), pressure, temperature,
group_idxs, barostat_interval,
seed + 1)
barostat_impl = barostat.impl(all_impls)
self.bound_impls = all_impls
self.barostat_impl = barostat_impl
self.lamb = lamb
self.n_steps = n_steps
def test_barostat_zero_interval():
pressure = 1.0 * unit.atmosphere
temperature = 300.0 * unit.kelvin
initial_waterbox_width = 2.5 * unit.nanometer
seed = 2021
np.random.seed(seed)
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))
afe = AbsoluteFreeEnergy(mol_a, ff)
unbound_potentials, sys_params, masses, coords = afe.prepare_host_edge(
ff.get_ordered_params(), complex_system, 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)
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)
with pytest.raises(RuntimeError):
custom_ops.MonteCarloBarostat(
coords.shape[0],
pressure.value_in_unit(unit.bar),
temperature.value_in_unit(unit.kelvin),
group_indices,
0,
u_impls,
seed,
)
# Setting it to 1 should be valid.
baro = custom_ops.MonteCarloBarostat(
coords.shape[0],
pressure.value_in_unit(unit.bar),
temperature.value_in_unit(unit.kelvin),
group_indices,
1,
u_impls,
seed,
)
# Setting back to 0 should raise another error
with pytest.raises(RuntimeError):
baro.set_interval(0)
def binding_model(ff_params):
dGs = []
for host_system, host_coords, host_box in [
(complex_system, complex_coords, complex_box),
(solvent_system, solvent_coords, solvent_box),
]:
# minimize the host to avoid clashes
host_coords = minimizer.minimize_host_4d([mol_a], host_system,
host_coords, ff, host_box)
unbound_potentials, sys_params, masses, coords = rfe.prepare_host_edge(
ff_params, host_system, host_coords)
x0 = coords
v0 = np.zeros_like(coords)
client = CUDAPoolClient(1)
harmonic_bond_potential = unbound_potentials[0]
group_idxs = get_group_indices(
get_bond_list(harmonic_bond_potential))
temperature = 300.0
pressure = 1.0
integrator = LangevinIntegrator(temperature, 1.5e-3, 1.0, masses,
seed)
barostat = MonteCarloBarostat(x0.shape[0], pressure, temperature,
group_idxs, 25, seed)
model = estimator.FreeEnergyModel(
unbound_potentials,
client,
host_box,
x0,
v0,
integrator,
lambda_schedule,
equil_steps,
prod_steps,
barostat,
)
dG, _ = estimator.deltaG(model, sys_params)
dGs.append(dG)
return dGs[0] - dGs[1]
def equilibrate_solvent_phase(
ubps,
params,
masses,
coords, # minimized_coords
box,
temperature,
pressure,
num_steps,
seed=None,
):
"""
Generate samples in the solvent phase.
"""
dt = 1e-4
friction = 1.0
bps = []
for p, bp in zip(params, ubps):
bps.append(bp.bind(p))
all_impls = [bp.bound_impl(np.float32) for bp in bps]
intg_equil = lib.LangevinIntegrator(temperature, dt, friction, masses, seed)
intg_equil_impl = intg_equil.impl()
bond_list = get_bond_list(ubps[0])
group_idxs = get_group_indices(bond_list)
barostat_interval = 5
barostat = lib.MonteCarloBarostat(len(masses), pressure, temperature, group_idxs, barostat_interval, seed + 1)
barostat_impl = barostat.impl(all_impls)
# equilibration/minimization doesn't need a barostat
equil_ctxt = custom_ops.Context(coords, np.zeros_like(coords), box, intg_equil_impl, all_impls, barostat_impl)
lamb = 0.0
# TODO: revert to 50k
equil_schedule = np.ones(num_steps) * lamb
equil_ctxt.multiple_steps(equil_schedule)
x0 = equil_ctxt.get_x_t()
# (ytz): This has to be zeros_like for now since if we freeze ligand
# coordinates it would start to move during rejected moves.
v0 = np.zeros_like(x0)
return CoordsVelBox(x0, v0, equil_ctxt.get_box())
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)
for lam in lambdas:
thermostat = UnadjustedLangevinMove(integrator_impl,
potential_energy_model.all_impls,
lam,
n_steps=barostat_interval)
barostat = MonteCarloBarostat(partial(reduced_potential_fxn, lam=lam),
group_indices,
def simulate_futures(
self,
ff_params,
mol,
x0,
box0,
prefix,
core_idxs=None,
seed=0
) -> Tuple[List[Any], estimator_abfe.FreeEnergyModel, List[Any]]:
top = self.setup_topology(mol)
afe = free_energy_rabfe.AbsoluteFreeEnergy(mol, top)
unbound_potentials, sys_params, masses = afe.prepare_host_edge(
ff_params, self.host_system)
if seed == 0:
seed = np.random.randint(np.iinfo(np.int32).max)
beta = 1 / (constants.BOLTZ * self.temperature)
bond_list = get_bond_list(unbound_potentials[0])
masses = model_utils.apply_hmr(masses, bond_list)
friction = 1.0
integrator = LangevinIntegrator(self.temperature, self.dt, friction,
masses, seed)
group_indices = get_group_indices(bond_list)
barostat_interval = 5
barostat = MonteCarloBarostat(x0.shape[0], self.pressure,
self.temperature, group_indices,
barostat_interval, seed)
v0 = np.zeros_like(x0)
endpoint_correct = False
model = estimator_abfe.FreeEnergyModel(
unbound_potentials,
endpoint_correct,
self.client,
box0,
x0,
v0,
integrator,
barostat,
self.host_schedule,
self.equil_steps,
self.prod_steps,
beta,
prefix,
)
bound_potentials = []
for params, unbound_pot in zip(sys_params, model.unbound_potentials):
bp = unbound_pot.bind(np.asarray(params))
bound_potentials.append(bp)
all_args = []
for lamb_idx, lamb in enumerate(model.lambda_schedule):
subsample_interval = 1000
all_args.append((
lamb,
model.box,
model.x0,
model.v0,
bound_potentials,
model.integrator,
model.barostat,
model.equil_steps,
model.prod_steps,
subsample_interval,
subsample_interval,
model.lambda_schedule,
))
if endpoint_correct:
assert isinstance(bound_potentials[-1], potentials.HarmonicBond)
all_args.append((
1.0,
model.box,
model.x0,
model.v0,
bound_potentials[:-1], # strip out the restraints
model.integrator,
model.barostat,
model.equil_steps,
model.prod_steps,
subsample_interval,
subsample_interval,
[], # no need to evaluate Us for the endpoint correction
))
futures = []
if self.client is None:
for args in all_args:
futures.append(_MockFuture(estimator_abfe.simulate(*args)))
else:
for args in all_args:
futures.append(
self.client.submit(estimator_abfe.simulate, *args))
return sys_params, model, futures
def equilibrate_edges(
self,
edges: List[Tuple[Chem.Mol, Chem.Mol, np.ndarray]],
lamb: float = 0.0,
barostat_interval: int = 10,
equilibration_steps: int = 100000,
cache_path: str = "equilibration_cache.pkl",
):
"""
edges: List of tuples with mol_a, mol_b, core
Edges to equilibrate
lamb: float
Lambda value to equilibrate at. Uses Dual Topology to equilibrate
barostat_interval: int
Interval on which to run barostat during equilibration
equilibration_steps: int
Number of steps to equilibrate the edge for
cache_path: string
Path to look for existing cache or path to where to save cache. By default
it will write out a pickle file in the local directory.
Pre equilibrate edges and cache them for later use in predictions.
Parallelized via the model client if possible
"""
if not self.pre_equilibrate:
return
if os.path.isfile(cache_path):
with open(cache_path, "rb") as ifs:
self._equil_cache = load(ifs)
print("Loaded Pre-equilibrated structures from cache")
return
futures = []
ordered_params = self.ff.get_ordered_params()
temperature = 300.0
pressure = 1.0
for stage, host_system, host_coords, host_box in [
("complex", self.complex_system, self.complex_coords,
self.complex_box),
("solvent", self.solvent_system, self.solvent_coords,
self.solvent_box),
]:
# Run all complex legs first then solvent, as they will likely take longer than then solvent leg
for mol_a, mol_b, core in edges:
# Use DualTopology to ensure mols exist in the same space.
topo = topology.DualTopologyMinimization(mol_a, mol_b, self.ff)
rfe = free_energy.RelativeFreeEnergy(topo)
min_coords = minimizer.minimize_host_4d([mol_a, mol_b],
host_system,
host_coords, self.ff,
host_box)
unbound_potentials, sys_params, masses, coords = rfe.prepare_host_edge(
ordered_params, host_system, min_coords)
# num_host_coords = len(host_coords)
# masses[num_host_coords:] *= 1000000 # Lets see if masses are the difference
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
group_idxs = get_group_indices(bond_list)
time_step = 1.5e-3
if self.hmr:
masses = apply_hmr(masses, bond_list)
time_step = 2.5e-3
integrator = LangevinIntegrator(temperature, time_step, 1.0,
masses, 0)
barostat = MonteCarloBarostat(coords.shape[0], pressure,
temperature, group_idxs,
barostat_interval, 0)
pots = []
for bp, params in zip(unbound_potentials, sys_params):
pots.append(bp.bind(np.asarray(params)))
future = self.client.submit(
estimator.equilibrate, *[
integrator, barostat, pots, coords, host_box, lamb,
equilibration_steps
])
futures.append((stage, (mol_a, mol_b, core), future))
num_equil = len(futures)
for i, (stage, edge, future) in enumerate(futures):
edge_hash = self._edge_hash(stage, *edge)
self._equil_cache[edge_hash] = future.result()
if (i + 1) % 5 == 0:
print(f"Pre-equilibrated {i+1} of {num_equil} edges")
print(f"Pre-equilibrated {num_equil} edges")
if cache_path:
with open(cache_path, "wb") as ofs:
dump(self._equil_cache, ofs)
print(f"Saved equilibration_cache to {cache_path}")
def predict(self, ff_params: list, mol_a: Chem.Mol, mol_b: Chem.Mol,
core: np.ndarray):
"""
Predict the ddG of morphing mol_a into mol_b. This function is differentiable w.r.t. ff_params.
Parameters
----------
ff_params: list of np.ndarray
This should match the ordered params returned by the forcefield
mol_a: Chem.Mol
Starting molecule corresponding to lambda = 0
mol_b: Chem.Mol
Starting molecule corresponding to lambda = 1
core: np.ndarray
N x 2 list of ints corresponding to the atom mapping of the core.
Returns
-------
float
delta delta G in kJ/mol
aux
list of TI results
"""
stage_dGs = []
stage_results = []
for stage, host_system, host_coords, host_box, lambda_schedule in [
("complex", self.complex_system, self.complex_coords,
self.complex_box, self.complex_schedule),
("solvent", self.solvent_system, self.solvent_coords,
self.solvent_box, self.solvent_schedule),
]:
single_topology = topology.SingleTopology(mol_a, mol_b, core,
self.ff)
rfe = free_energy.RelativeFreeEnergy(single_topology)
edge_hash = self._edge_hash(stage, mol_a, mol_b, core)
if self.pre_equilibrate and edge_hash in self._equil_cache:
cached_state = self._equil_cache[edge_hash]
x0 = cached_state.coords
host_box = cached_state.box
num_host_coords = len(host_coords)
unbound_potentials, sys_params, masses, _ = rfe.prepare_host_edge(
ff_params, host_system, host_coords)
mol_a_size = mol_a.GetNumAtoms()
# Use Dual Topology to pre equilibrate, so have to get the mean of the two sets of mol,
# normally done within prepare_host_edge, but the whole system has moved by this stage
x0 = np.concatenate([
x0[:num_host_coords],
np.mean(
single_topology.interpolate_params(
x0[num_host_coords:num_host_coords + mol_a_size],
x0[num_host_coords + mol_a_size:]),
axis=0,
),
])
else:
if self.pre_equilibrate:
print(
"Edge not correctly pre-equilibrated, ensure equilibrate_edges was called"
)
print(
f"Minimizing the {stage} host structure to remove clashes."
)
# (ytz): this isn't strictly symmetric, and we should modify minimize later on remove
# the hysteresis by jointly minimizing against a and b at the same time. We may also want
# to remove the randomness completely from the minimization.
min_host_coords = minimizer.minimize_host_4d([mol_a, mol_b],
host_system,
host_coords,
self.ff, host_box)
unbound_potentials, sys_params, masses, coords = rfe.prepare_host_edge(
ff_params, host_system, min_host_coords)
x0 = coords
v0 = np.zeros_like(x0)
time_step = 1.5e-3
harmonic_bond_potential = unbound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
if self.hmr:
masses = apply_hmr(masses, bond_list)
time_step = 2.5e-3
group_idxs = get_group_indices(bond_list)
seed = 0
temperature = 300.0
pressure = 1.0
integrator = LangevinIntegrator(temperature, time_step, 1.0,
masses, seed)
barostat = MonteCarloBarostat(x0.shape[0], pressure, temperature,
group_idxs, self.barostat_interval,
seed)
model = estimator.FreeEnergyModel(
unbound_potentials,
self.client,
host_box,
x0,
v0,
integrator,
lambda_schedule,
self.equil_steps,
self.prod_steps,
barostat,
)
dG, results = estimator.deltaG(model, sys_params)
stage_dGs.append(dG)
stage_results.append((stage, results))
pred = stage_dGs[0] - stage_dGs[1]
return pred, stage_results
def benchmark(
label,
masses,
lamb,
x0,
v0,
box,
bound_potentials,
hmr=False,
verbose=True,
num_batches=100,
steps_per_batch=1000,
compute_du_dl_interval=0,
barostat_interval=0,
):
"""
TODO: configuration blob containing num_batches, steps_per_batch, and any other options
"""
seed = 1234
dt = 1.5e-3
temperature = 300
pressure = 1.0
seconds_per_day = 86400
harmonic_bond_potential = bound_potentials[0]
bond_list = get_bond_list(harmonic_bond_potential)
if hmr:
dt = 2.5e-3
masses = apply_hmr(masses, bond_list)
intg = LangevinIntegrator(temperature, dt, 1.0, np.array(masses), seed).impl()
bps = []
for potential in bound_potentials:
bps.append(potential.bound_impl(precision=np.float32)) # get the bound implementation
baro_impl = None
if barostat_interval > 0:
group_idxs = get_group_indices(bond_list)
baro = MonteCarloBarostat(
x0.shape[0],
pressure,
temperature,
group_idxs,
barostat_interval,
seed,
)
baro_impl = baro.impl(bps)
ctxt = custom_ops.Context(
x0,
v0,
box,
intg,
bps,
barostat=baro_impl,
)
batch_times = []
lambda_schedule = np.ones(steps_per_batch) * lamb
# run once before timer starts
ctxt.multiple_steps(lambda_schedule, compute_du_dl_interval)
start = time.time()
for batch in range(num_batches):
# time the current batch
batch_start = time.time()
du_dls, _, _ = ctxt.multiple_steps(lambda_schedule, compute_du_dl_interval)
batch_end = time.time()
delta = batch_end - batch_start
batch_times.append(delta)
steps_per_second = steps_per_batch / np.mean(batch_times)
steps_per_day = steps_per_second * seconds_per_day
ps_per_day = dt * steps_per_day
ns_per_day = ps_per_day * 1e-3
if verbose:
print(f"steps per second: {steps_per_second:.3f}")
print(f"ns per day: {ns_per_day:.3f}")
assert np.all(np.abs(ctxt.get_x_t()) < 1000)
print(
f"{label}: N={x0.shape[0]} speed: {ns_per_day:.2f}ns/day dt: {dt*1e3}fs (ran {steps_per_batch * num_batches} steps in {(time.time() - start):.2f}s)"
)
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_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_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_free_energy_estimator_with_endpoint_correction():
"""
Test that we generate correctly shaped derivatives in the estimator code
when the endpoint correction is turned on. We expected that f([a,b,c,...])
to generate derivatives df/da, df/db, df/dc, df/d... such that
df/da.shape == a.shape, df/db.shape == b.shape, df/dc == c.shape, and etc.
"""
n_atoms = 15
x0 = np.random.rand(n_atoms, 3)
v0 = np.zeros_like(x0)
n_bonds = 3
n_angles = 4
n_restraints = 5
hb_pot, hb_params = get_harmonic_bond(n_atoms, n_bonds)
ha_pot, ha_params = get_harmonic_angle(n_atoms, n_angles)
rs_pot, rs_params = get_harmonic_restraints(n_atoms, n_restraints)
sys_params = [hb_params, ha_params, rs_params]
unbound_potentials = [hb_pot, ha_pot, rs_pot]
masses = np.random.rand(n_atoms)
box = np.eye(3, dtype=np.float64)
seed = 2021
group_idxs = get_group_indices(get_bond_list(hb_pot))
temperature = 300.0
pressure = 1.0
integrator = LangevinIntegrator(temperature, 1.5e-3, 1.0, masses, seed)
barostat = MonteCarloBarostat(x0.shape[0], pressure, temperature,
group_idxs, 25, seed)
beta = 0.125
lambda_schedule = np.linspace(0, 1.0, 4)
def loss_fn(sys_params):
endpoint_correct = True
mdl = estimator_abfe.FreeEnergyModel(
unbound_potentials,
endpoint_correct,
client,
box,
x0,
v0,
integrator,
barostat,
lambda_schedule,
100,
100,
beta,
"test",
)
dG, bar_dG_err, results = estimator_abfe.deltaG(mdl, sys_params)
return dG**2
for client in [None, CUDAPoolClient(1)]:
loss_fn(sys_params)
def equilibrate_host(
mol: Chem.Mol,
host_system: openmm.System,
host_coords: NDArray,
temperature: float,
pressure: float,
ff: Forcefield,
box: NDArray,
n_steps: int,
seed: Optional[int] = None,
) -> Tuple[NDArray, NDArray]:
"""
Equilibrate a host system given a reference molecule using the MonteCarloBarostat.
Useful for preparing a host that will be used for multiple FEP calculations using the same reference, IE a starmap.
Performs the following:
- Minimize host with rigid mol
- Minimize host and mol
- Run n_steps with HMR enabled and MonteCarloBarostat every 5 steps
Parameters
----------
mol: Chem.Mol
Ligand for the host to equilibrate with.
host_system: openmm.System
OpenMM System representing the host.
host_coords: np.ndarray
N x 3 coordinates of the host. units of nanometers.
temperature: float
Temperature at which to run the simulation. Units of kelvins.
pressure: float
Pressure at which to run the simulation. Units of bars.
ff: ff.Forcefield
Wrapper class around a list of handlers.
box: np.ndarray [3,3]
Box matrix for periodic boundary conditions. units of nanometers.
n_steps: int
Number of steps to run the simulation for.
seed: int or None
Value to seed simulation with
Returns
-------
tuple (coords, box)
Returns equilibrated system coords as well as the box.
"""
# insert mol into the binding pocket.
host_bps, host_masses = openmm_deserializer.deserialize_system(host_system, cutoff=1.2)
min_host_coords = minimize_host_4d([mol], host_system, host_coords, ff, box)
ligand_masses = [a.GetMass() for a in mol.GetAtoms()]
ligand_coords = get_romol_conf(mol)
combined_masses = np.concatenate([host_masses, ligand_masses])
combined_coords = np.concatenate([min_host_coords, ligand_coords])
top = topology.BaseTopology(mol, ff)
hgt = topology.HostGuestTopology(host_bps, top)
# setup the parameter handlers for the ligand
tuples = [
[hgt.parameterize_harmonic_bond, [ff.hb_handle]],
[hgt.parameterize_harmonic_angle, [ff.ha_handle]],
[hgt.parameterize_periodic_torsion, [ff.pt_handle, ff.it_handle]],
[hgt.parameterize_nonbonded, [ff.q_handle, ff.lj_handle]],
]
u_impls = []
bound_potentials = []
for fn, handles in tuples:
params, potential = fn(*[h.params for h in handles])
bp = potential.bind(params)
bound_potentials.append(bp)
u_impls.append(bp.bound_impl(precision=np.float32))
bond_list = get_bond_list(bound_potentials[0])
combined_masses = model_utils.apply_hmr(combined_masses, bond_list)
dt = 2.5e-3
friction = 1.0
if seed is None:
seed = np.random.randint(np.iinfo(np.int32).max)
integrator = LangevinIntegrator(temperature, dt, friction, combined_masses, seed).impl()
x0 = combined_coords
v0 = np.zeros_like(x0)
group_indices = get_group_indices(bond_list)
barostat_interval = 5
barostat = MonteCarloBarostat(x0.shape[0], pressure, temperature, group_indices, barostat_interval, seed).impl(
u_impls
)
# Re-minimize with the mol being flexible
x0 = fire_minimize(x0, u_impls, box, np.ones(50))
# context components: positions, velocities, box, integrator, energy fxns
ctxt = custom_ops.Context(x0, v0, box, integrator, u_impls, barostat)
ctxt.multiple_steps(np.linspace(0.0, 0.0, n_steps))
return ctxt.get_x_t(), ctxt.get_box()
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)
