def setup(self):
import openpathsampling.engines.toy as toys
# applies one delta_v to all atoms
self.toy_modifier_all = GeneralizedDirectionModifier(1.5)
# defines delta_v per atom, including those not in the mask
self.toy_modifier_long_dv = GeneralizedDirectionModifier(
delta_v=[0.5, 1.0, 2.0], subset_mask=[1, 2])
# defines delta_v per atom in the subset mask
self.toy_modifier = GeneralizedDirectionModifier(delta_v=[1.0, 2.0],
subset_mask=[1, 2])
self.toy_engine = toys.Engine(topology=toys.Topology(
n_spatial=2, n_atoms=3, pes=None, masses=[1.0, 1.5, 4.0]),
options={})
self.toy_snapshot = toys.Snapshot(coordinates=np.array([[0.0, 0.0],
[0.0, 0.0],
[0.0, 0.0]]),
velocities=np.array([[1.0, 1.0],
[2.0, 2.0],
[3.0, 3.0]]),
engine=self.toy_engine)
# create the OpenMM versions
u_vel = old_div(u.nanometer, u.picosecond)
self.openmm_modifier = GeneralizedDirectionModifier(1.2 * u_vel)
ad_vacuum = omt.testsystems.AlanineDipeptideVacuum(constraints=None)
self.test_snap = omm_engine.snapshot_from_testsystem(ad_vacuum)
self.openmm_engine = omm_engine.Engine(
topology=self.test_snap.topology,
system=ad_vacuum.system,
integrator=omt.integrators.VVVRIntegrator())
self.openmm_snap = self.test_snap.copy_with_replacement(
engine=self.openmm_engine)
def setup(self):
import openpathsampling.engines.toy as toys
self.toy_modifier = SingleAtomVelocityDirectionModifier(
delta_v=[1.0, 2.0],
subset_mask=[1, 2],
remove_linear_momentum=False)
self.toy_engine = toys.Engine(
topology=toys.Topology(n_spatial=2,
n_atoms=3,
pes=None,
masses=np.array([1.0, 1.5, 4.0])),
options={})
self.toy_snapshot = toys.Snapshot(coordinates=np.array([[0.0, 0.0],
[0.0, 0.0],
[0.0, 0.0]]),
velocities=np.array([[1.0, 1.0],
[2.0, 2.0],
[3.0, 3.0]]),
engine=self.toy_engine)
u_vel = old_div(u.nanometer, u.picosecond)
self.openmm_modifier = SingleAtomVelocityDirectionModifier(
delta_v=1.2 * u_vel, remove_linear_momentum=False)
ad_vacuum = omt.testsystems.AlanineDipeptideVacuum(constraints=None)
self.test_snap = omm_engine.snapshot_from_testsystem(ad_vacuum)
self.openmm_engine = omm_engine.Engine(
topology=self.test_snap.topology,
system=ad_vacuum.system,
integrator=omt.integrators.VVVRIntegrator())
self.openmm_snap = self.test_snap.copy_with_replacement(
engine=self.openmm_engine,
velocities=np.ones(shape=self.test_snap.velocities.shape) * u_vel)
def build_engine(self):
"""Builds the OpenMMEngine."""
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
kinase = self.kinase
#### SET UP THE OPENMM STUFF #######################################
# taken from builder.openmm.org
forcefield = app.ForceField('amber99sbildn.xml', 'amber99_obc.xml')
system = forcefield.createSystem(app.PDBFile(kinase['pdb']).topology,
nonbondedMethod=app.NoCutoff,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(300 * unit.kelvin,
1.0 / unit.picoseconds,
2.0 * unit.femtoseconds)
integrator.setConstraintTolerance(0.00001)
#### OPENPATHSAMPLING-SPECIFIC SETUP ###############################
options = {'nsteps_per_frame': 50, 'n_frames_max': 1500}
template = omm_eng.tools.snapshot_from_pdb(kinase['pdb'])
engine = omm_eng.Engine(template=template,
system=system,
integrator=integrator,
options=options)
return engine
def setup(self):
# OpenMM Integrator
integrator = mm.LangevinIntegrator(
300*u.kelvin,
old_div(1.0,u.picoseconds),
2.0*u.femtoseconds
)
integrator.setConstraintTolerance(0.00001)
# Engine options
options = {
'n_steps_per_frame': 2,
'n_frames_max': 5
}
self.engine = peng.Engine(
template.topology,
system,
integrator,
options=options
)
self.engine.initialize('CPU')
context = self.engine.simulation.context
zero_array = np.zeros((template.topology.n_atoms, 3))
context.setPositions(template.coordinates)
context.setVelocities(u.Quantity(zero_array, old_div(u.nanometers, u.picoseconds)))
def test_verify_snapshot_constraints(self):
ad_vacuum_constr = omt.testsystems.AlanineDipeptideVacuum()
constrained_engine = omm_engine.Engine(
topology=self.test_snap.topology,
system=ad_vacuum_constr.system,
integrator=omt.integrators.VVVRIntegrator())
constr_snap = self.test_snap.copy_with_replacement(
engine=constrained_engine)
self.openmm_modifier._verify_snapshot(constr_snap)
def setup(self):
test_system = omt.testsystems.AlanineDipeptideVacuum()
self.template = omm_engine.snapshot_from_testsystem(test_system)
self.engine = omm_engine.Engine(
topology=self.template.topology,
system=test_system.system,
integrator=omt.integrators.VVVRIntegrator())
self.n_atoms = self.engine.topology.n_atoms
self.engine.current_snapshot = self.template
def test_verify_snapshot_box_vectors(self):
ad_explicit = omt.testsystems.AlanineDipeptideExplicit(
constraints=None, rigid_water=False)
ad_explicit_tmpl = omm_engine.snapshot_from_testsystem(ad_explicit)
explicit_engine = omm_engine.Engine(
topology=ad_explicit_tmpl.topology,
system=ad_explicit.system,
integrator=omt.integrators.VVVRIntegrator())
ad_explicit_snap = ad_explicit_tmpl.copy_with_replacement(
engine=explicit_engine)
self.openmm_modifier._verify_snapshot(ad_explicit_snap)
def test_has_constraints(self, has_constraints):
omt = pytest.importorskip('openmmtools')
constraints = app.HBonds if has_constraints else None
system = omt.testsystems.AlanineDipeptideVacuum(
constraints=constraints
)
template = peng.snapshot_from_testsystem(system)
engine = peng.Engine(
topology=template.topology,
system=system.system,
integrator=omt.integrators.VVVRIntegrator()
)
assert engine.has_constraints() == has_constraints
def setup(self):
if not openmm:
raise SkipTest("OpenMM not installed")
if not omt:
raise SkipTest("OpenMMTools not installed; required for OpenMM "
"tests.")
self.test_system = omt.testsystems.AlanineDipeptideVacuum()
self.template = omm_engine.snapshot_from_testsystem(self.test_system)
self.engine = omm_engine.Engine(
topology=self.template.topology,
system=self.test_system.system,
integrator=omt.integrators.VVVRIntegrator()
)
self.n_atoms = self.engine.topology.n_atoms
self.engine.current_snapshot = self.template
def run_steps(steps):
template = peng.snapshot_from_pdb(
"/Users/jan-hendrikprinz/Studium/git/openpathsampling/examples/data/Alanine_solvated.pdb")
topology = peng.to_openmm_topology(template)
# Generated using OpenMM Script Builder
# http://builder.openmm.org
forcefield = mm.app.ForceField(
'amber96.xml', # solute FF
'tip3p.xml' # solvent FF
)
# OpenMM System
system = forcefield.createSystem(
topology,
nonbondedMethod=mm.app.PME,
nonbondedCutoff=1.0*u.nanometers,
constraints=mm.app.HBonds,
ewaldErrorTolerance=0.0005
)
# OpenMM Integrator
integrator = mm.LangevinIntegrator(
300 * u.kelvin,
1.0 / u.picoseconds,
2.0 * u.femtoseconds
)
integrator.setConstraintTolerance(0.00001)
# Engine options
options = {
'n_steps_per_frame': 2,
'n_frames_max': 5
}
engine = peng.Engine(
template.topology,
system,
integrator,
options=options
)
engine.initialize('CPU')
traj = engine.generate(template, paths.LengthEnsemble(steps).can_append)
return traj
def test_with_openmm_snapshot(self):
# note: this is only a smoke test; correctness depends on OpenMM's
# tests of its constraint approaches.
if not omt:
raise SkipTest("Requires OpenMMTools (not installed)")
test_system = omt.testsystems.AlanineDipeptideVacuum()
template = omm_engine.snapshot_from_testsystem(test_system)
engine = omm_engine.Engine(
topology=template.topology,
system=test_system.system,
integrator=omt.integrators.VVVRIntegrator()
)
beta = old_div(1.0, (300.0 * u.kelvin * u.BOLTZMANN_CONSTANT_kB))
# when the engine doesn't have an existing snapshot
randomizer = RandomVelocities(beta=beta, engine=engine)
new_snap = randomizer(template)
# coordinates stayed the same
assert_array_almost_equal(template.coordinates,
new_snap.coordinates)
# velocities changed
assert_equal(np.isclose(template.velocities,
new_snap.velocities).all(),
False)
engine.generate(new_snap, [lambda x, foo: len(x) <= 4])
# when the engine does have an existing snapshot
zeros = np.zeros((engine.n_atoms, engine.n_spatial))
zero_snap = paths.engines.openmm.Snapshot.construct(
coordinates=zeros * u.nanometer,
velocities=zeros * u.nanometer / u.picosecond,
box_vectors=template.box_vectors,
engine=engine
)
engine.current_snapshot = zero_snap
randomizer = RandomVelocities(beta=beta, engine=engine)
new_snap = randomizer(template)
# coordinates stayed the same
assert_array_almost_equal(template.coordinates,
new_snap.coordinates)
# velocities changed
assert_equal(np.isclose(template.velocities,
new_snap.velocities).all(),
False)
# internal snapshot unchanged
assert_equal(engine.current_snapshot, zero_snap)
engine.generate(new_snap, [lambda x, foo: len(x) <= 4])
def test_verify_engine_constraints(self):
ad_vacuum_constr = omt.testsystems.AlanineDipeptideVacuum()
constrained_engine = omm_engine.Engine(
topology=self.test_snap.topology,
system=ad_vacuum_constr.system,
integrator=omt.integrators.VVVRIntegrator())
modifier = GeneralizedDirectionModifier(1.2 * u.nanometer /
u.picosecond,
engine=constrained_engine)
# this is a hack because ndofs not defined in TestsystemEngine
self.openmm_engine.current_snapshot = self.test_snap
snap = self.openmm_engine.current_snapshot
# when it checks based on the engine, it should be fine
self.openmm_modifier._verify_snapshot(snap)
# when modifier overrides snap.engine, it errors
with pytest.raises(RuntimeError, match="constraints"):
modifier._verify_snapshot(snap)
def setup(self):
if not openmm:
raise SkipTest("OpenMM not installed")
if not omt:
raise SkipTest("OpenMMTools not installed; required for OpenMM "
"tests.")
self.test_system = omt.testsystems.AlanineDipeptideVacuum()
self.template = omm_engine.snapshot_from_testsystem(self.test_system)
self.engine = omm_engine.Engine(
topology=self.template.topology,
system=self.test_system.system,
integrator=omt.integrators.VVVRIntegrator())
self.n_atoms = self.engine.topology.n_atoms
self.test_snap = omm_engine.Snapshot.construct(
coordinates=self.template.coordinates,
box_vectors=self.template.box_vectors,
velocities=self.template.velocities,
engine=self.engine)
pdb = app.PDBFile('../../porin-ligand.pdb')
integrator = openmm.LangevinIntegrator(310 * unit.kelvin,
1.0 / unit.picoseconds,
4 * unit.femtosecond)
with open('../../arg/openmm_system_tps.xml', 'r') as infile:
openmm_system = XmlSerializer.deserialize(infile.read())
template = ops_load_trajectory('../../porin-ligand.pdb')[0]
openmm_properties = {'CUDAPrecision': 'mixed'}
engine_options = {'n_steps_per_frame': 500, 'n_frames_max': 10000}
engine = omm.Engine(template.topology,
openmm_system,
integrator,
openmm_properties=openmm_properties,
options=engine_options).named("arg_engine")
topology = md.Topology.from_openmm(pdb.topology)
bottom_atoms = [1396, 5018, 3076]
top_atoms = [6241, 3325, 1626]
selection = '(residue 422) and (mass > 3.0)'
ligand_atoms = topology.select(selection)
groups = [bottom_atoms] + [top_atoms] + [ligand_atoms]
# Defining the CVs
cv_r_p = FunctionCV('r_p',
r_parallel,
topology=topology,
groups=groups,
print("Selecting a platform...")
platform_name = 'CUDA'
platform = openmm.Platform.getPlatformByName(platform_name)
openmm_properties = {'OpenCLPrecision': 'mixed'}
# Create an engine
print('Creating engine...')
engine_options = {
'n_frames_max': 1000,
'platform': platform_name,
'n_steps_per_frame': 50
}
engine = engine.Engine(template.topology,
system,
integrator,
openmm_properties=openmm_properties,
options=engine_options)
engine.name = 'default'
# Create a hot engine for generating an initial unbinding path
print('Creating a "hot" engine...')
integrator_hot = VVVRIntegrator(temperature_hot, collision_rate, timestep)
integrator_hot.setConstraintTolerance(1.0e-6)
engine_hot = engine.from_new_options(integrator=integrator_hot)
engine_hot.name = 'hot'
# Select engine mover
paths.EngineMover.engine = engine
# Create storage
