def setUp(self):
prmtop = app.AmberPrmtopFile('systems/water-box-216.prmtop')
system = prmtop.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=0.9 * unit.nanometers,
constraints=app.HBonds,
rigidWater=True,
ewaldErrorTolerance=0.0005)
integrator = mm.LangevinIntegrator(300 * unit.kelvin,
1.0 / unit.picoseconds,
2.0 * unit.femtoseconds)
self.simulation = app.Simulation(
prmtop.topology, system, integrator,
mm.Platform.getPlatformByName('Reference'))
def _configure_amber_implicit(
pdb_file: PathLike,
top_file: Optional[PathLike],
dt_ps: float,
temperature_kelvin: float,
heat_bath_friction_coef: float,
platform: "openmm.Platform",
platform_properties: dict,
) -> Tuple["app.Simulation", Optional["app.PDBFile"]]:
# Configure system
if top_file is not None:
pdb = None
top = app.AmberPrmtopFile(str(top_file))
system = top.createSystem(
nonbondedMethod=app.CutoffNonPeriodic,
nonbondedCutoff=1.0 * u.nanometer,
constraints=app.HBonds,
implicitSolvent=app.OBC1,
)
else:
pdb = app.PDBFile(str(pdb_file))
top = pdb.topology
forcefield = app.ForceField("amber99sbildn.xml", "amber99_obc.xml")
system = forcefield.createSystem(
top,
nonbondedMethod=app.CutoffNonPeriodic,
nonbondedCutoff=1.0 * u.nanometer,
constraints=app.HBonds,
)
# Configure integrator
integrator = openmm.LangevinIntegrator(
temperature_kelvin * u.kelvin,
heat_bath_friction_coef / u.picosecond,
dt_ps * u.picosecond,
)
integrator.setConstraintTolerance(0.00001)
sim = app.Simulation(top, system, integrator, platform,
platform_properties)
# Returning the pdb file object for later use to reduce I/O.
# If a topology file is passed, the pdb variable is None.
return sim, pdb
def _configure_amber_explicit(
top_file: PathLike,
dt_ps: float,
temperature_kelvin: float,
heat_bath_friction_coef: float,
platform: "openmm.Platform",
platform_properties: dict,
explicit_barostat: str,
) -> "app.Simulation":
top = app.AmberPrmtopFile(str(top_file))
system = top.createSystem(
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * u.nanometer,
constraints=app.HBonds,
)
# Congfigure integrator
integrator = openmm.LangevinIntegrator(
temperature_kelvin * u.kelvin,
heat_bath_friction_coef / u.picosecond,
dt_ps * u.picosecond,
)
if explicit_barostat == "MonteCarloBarostat":
system.addForce(
openmm.MonteCarloBarostat(1 * u.bar,
temperature_kelvin * u.kelvin))
elif explicit_barostat == "MonteCarloAnisotropicBarostat":
system.addForce(
openmm.MonteCarloAnisotropicBarostat(
(1, 1, 1) * u.bar, temperature_kelvin * u.kelvin, False, False,
True))
else:
raise ValueError(
f"Invalid explicit_barostat option: {explicit_barostat}")
sim = app.Simulation(top.topology, system, integrator, platform,
platform_properties)
return sim
def create_openmm_system(sim_openmm,
model,
anchor,
frame=0,
load_state_file=None):
"""
Create an openmm System() object.
"""
building_directory = os.path.join(model.anchor_rootdir, anchor.directory,
anchor.building_directory)
box_vectors = None
num_frames = 0
positions_obj = None
if anchor.__class__.__name__ in ["MMVT_toy_anchor", "Elber_toy_anchor"]:
if load_state_file is not None:
positions = None
num_frames = 1
elif anchor.starting_positions is not None:
positions_frames = np.array(anchor.starting_positions) \
* openmm.unit.nanometers
positions = positions_frames[frame]
num_frames = len(positions_frames)
else:
raise Exception(
"No starting state or starting positions provided.")
else:
if anchor.amber_params is not None:
prmtop_filename = os.path.join(building_directory,
anchor.amber_params.prmtop_filename)
prmtop = openmm_app.AmberPrmtopFile(prmtop_filename)
#assert anchor.amber_params.pdb_coordinates_filename is not None
if anchor.amber_params.pdb_coordinates_filename is None \
or anchor.amber_params.pdb_coordinates_filename == "":
positions_obj = None
positions = None
sim_openmm.try_to_load_state = True
else:
pdb_coordinates_filename = os.path.join(
building_directory,
anchor.amber_params.pdb_coordinates_filename)
positions_obj = openmm_app.PDBFile(pdb_coordinates_filename)
#assert anchor.amber_params.box_vectors is not None
box_vectors = anchor.amber_params.box_vectors
topology = prmtop.topology
elif anchor.forcefield_params is not None:
forcefield_filenames = []
for forcefield_filename in \
anchor.forcefield_params.built_in_forcefield_filenames:
forcefield_filenames.append(forcefield_filename)
for forcefield_filename in \
anchor.forcefield_params.custom_forcefield_filenames:
forcefield_filenames.append(
os.path.join(building_directory, forcefield_filename))
print("anchor.forcefield_params.pdb_filename:",
anchor.forcefield_params.pdb_coordinates_filename)
pdb_filename = os.path.join(
building_directory,
anchor.forcefield_params.pdb_coordinates_filename)
print("pdb_filename:", pdb_filename)
pdb = openmm_app.PDBFile(pdb_filename)
forcefield = openmm_app.ForceField(*forcefield_filenames)
box_vectors = anchor.forcefield_params.box_vectors
topology = pdb.topology
positions_obj = pdb
positions = None
elif anchor.charmm_params is not None:
raise Exception("Charmm systems not yet implemented")
else:
raise Exception("No Amber or Charmm input settings detected.")
#assert box_vectors is not None, "No source of box vectors provided."
nonbonded_method = model.openmm_settings.nonbonded_method.lower()
if nonbonded_method == "pme":
nonbondedMethod = openmm_app.PME
elif nonbonded_method == "nocutoff":
nonbondedMethod = openmm_app.NoCutoff
elif nonbonded_method == "cutoffnonperiodic":
nonbondedMethod = openmm_app.CutoffNonPeriodic
elif nonbonded_method == "cutoffperiodic":
nonbondedMethod = openmm_app.CutoffPeriodic
elif nonbonded_method == "ewald":
nonbondedMethod = openmm_app.Ewald
else:
raise Exception("nonbonded method not found: %s",
model.openmm_settings.nonbonded_method)
if model.openmm_settings.constraints is None:
constraints_str = None
else:
constraints_str = model.openmm_settings.constraints
if constraints_str is None:
constraints = None
elif constraints_str.lower() == "none":
constraints = None
elif constraints_str.lower() == "hbonds":
constraints = openmm_app.HBonds
elif constraints_str.lower() == "allbonds":
constraints = openmm_app.AllBonds
elif constraints_str.lower() == "hangles":
constraints = openmm_app.HAngles
else:
raise Exception("constraints not found: %s",
model.openmm_settings.constraints)
if model.openmm_settings.hydrogenMass is not None:
hydrogenMass = model.openmm_settings.hydrogenMass * openmm.unit.amu
else:
hydrogenMass = None
rigidWater = model.openmm_settings.rigidWater
if anchor.__class__.__name__ in ["MMVT_toy_anchor", "Elber_toy_anchor"]:
system, topology = make_toy_system_object(model)
else:
if anchor.amber_params is not None:
system = prmtop.createSystem(
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=model.openmm_settings.nonbonded_cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass,
rigidWater=rigidWater)
elif anchor.forcefield_params is not None:
system = forcefield.createSystem(
pdb.topology,
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=model.openmm_settings.nonbonded_cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass,
rigidWater=rigidWater)
elif anchor.charmm_params is not None:
raise Exception("Charmm input settings not yet implemented")
else:
print("Settings for Amber or Charmm simulations not found")
if positions_obj is not None:
positions = positions_obj.getPositions(frame=frame)
assert frame >= 0, "Cannot have negative frame index"
assert frame < positions_obj.getNumFrames(), \
"Frame index {} out of range.".format(frame)
num_frames = positions_obj.getNumFrames()
return system, topology, positions, box_vectors, num_frames
def runOneTest(testName, options):
"""Perform a single benchmarking simulation."""
explicit = (testName not in ('gbsa', 'amoebagk'))
amoeba = (testName in ('amoebagk', 'amoebapme'))
apoa1 = testName.startswith('apoa1')
amber = (testName.startswith('amber'))
hydrogenMass = None
print()
if amoeba:
print('Test: %s (epsilon=%g)' % (testName, options.epsilon))
elif testName == 'pme':
print('Test: pme (cutoff=%g)' % options.cutoff)
else:
print('Test: %s' % testName)
print('Ensemble: %s' % options.ensemble)
platform = mm.Platform.getPlatformByName(options.platform)
# Create the System.
temperature = 300 * unit.kelvin
if explicit:
friction = 1 * (1 / unit.picoseconds)
else:
friction = 91 * (1 / unit.picoseconds)
if amoeba:
constraints = None
epsilon = float(options.epsilon)
if explicit:
ff = app.ForceField('amoeba2009.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
cutoff = 0.7 * unit.nanometers
vdwCutoff = 0.9 * unit.nanometers
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=cutoff,
vdwCutoff=vdwCutoff,
constraints=constraints,
ewaldErrorTolerance=0.00075,
mutualInducedTargetEpsilon=epsilon,
polarization=options.polarization)
else:
ff = app.ForceField('amoeba2009.xml', 'amoeba2009_gk.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
cutoff = 2.0 * unit.nanometers
vdwCutoff = 1.2 * unit.nanometers
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.NoCutoff,
constraints=constraints,
mutualInducedTargetEpsilon=epsilon,
polarization=options.polarization)
for f in system.getForces():
if isinstance(f, mm.AmoebaMultipoleForce) or isinstance(
f, mm.AmoebaVdwForce) or isinstance(
f, mm.AmoebaGeneralizedKirkwoodForce) or isinstance(
f, mm.AmoebaWcaDispersionForce):
f.setForceGroup(1)
dt = 0.002 * unit.picoseconds
if options.ensemble == 'NVE':
integ = mm.MTSIntegrator(dt, [(0, 2), (1, 1)])
else:
integ = mm.MTSLangevinIntegrator(temperature, friction, dt,
[(0, 2), (1, 1)])
positions = pdb.positions
elif amber:
dirname = downloadAmberSuite()
names = {
'amber20-dhfr': 'JAC',
'amber20-factorix': 'FactorIX',
'amber20-cellulose': 'Cellulose',
'amber20-stmv': 'STMV'
}
fileName = names[testName]
prmtop = app.AmberPrmtopFile(
os.path.join(dirname, f'PME/Topologies/{fileName}.prmtop'))
inpcrd = app.AmberInpcrdFile(
os.path.join(dirname, f'PME/Coordinates/{fileName}.inpcrd'))
topology = prmtop.topology
positions = inpcrd.positions
dt = 0.004 * unit.picoseconds
method = app.PME
cutoff = options.cutoff
constraints = app.HBonds
system = prmtop.createSystem(nonbondedMethod=method,
nonbondedCutoff=cutoff,
constraints=constraints)
if options.ensemble == 'NVE':
integ = mm.VerletIntegrator(dt)
else:
integ = mm.LangevinMiddleIntegrator(temperature, friction, dt)
else:
if apoa1:
ff = app.ForceField('amber14/protein.ff14SB.xml',
'amber14/lipid17.xml', 'amber14/tip3p.xml')
pdb = app.PDBFile('apoa1.pdb')
if testName == 'apoa1pme':
method = app.PME
cutoff = options.cutoff
elif testName == 'apoa1ljpme':
method = app.LJPME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
hydrogenMass = 1.5 * unit.amu
elif explicit:
ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
if testName == 'pme':
method = app.PME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
else:
ff = app.ForceField('amber99sb.xml', 'amber99_obc.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
method = app.CutoffNonPeriodic
cutoff = 2 * unit.nanometers
if options.heavy:
dt = 0.005 * unit.picoseconds
constraints = app.AllBonds
hydrogenMass = 4 * unit.amu
if options.ensemble == 'NVE':
integ = mm.VerletIntegrator(dt)
else:
integ = mm.LangevinIntegrator(temperature, friction, dt)
else:
dt = 0.004 * unit.picoseconds
constraints = app.HBonds
if options.ensemble == 'NVE':
integ = mm.VerletIntegrator(dt)
else:
integ = mm.LangevinMiddleIntegrator(temperature, friction, dt)
positions = pdb.positions
system = ff.createSystem(pdb.topology,
nonbondedMethod=method,
nonbondedCutoff=cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass)
if options.ensemble == 'NPT':
system.addForce(mm.MonteCarloBarostat(1 * unit.bar, temperature, 100))
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
properties = {}
initialSteps = 5
if options.device is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['DeviceIndex'] = options.device
if ',' in options.device or ' ' in options.device:
initialSteps = 250
if options.precision is not None and platform.getName() in ('CUDA',
'OpenCL'):
properties['Precision'] = options.precision
# Run the simulation.
integ.setConstraintTolerance(1e-5)
if len(properties) > 0:
context = mm.Context(system, integ, platform, properties)
else:
context = mm.Context(system, integ, platform)
context.setPositions(positions)
if amber:
if inpcrd.boxVectors is not None:
context.setPeriodicBoxVectors(*inpcrd.boxVectors)
mm.LocalEnergyMinimizer.minimize(
context, 100 * unit.kilojoules_per_mole / unit.nanometer)
context.setVelocitiesToTemperature(temperature)
steps = 20
while True:
time = timeIntegration(context, steps, initialSteps)
if time >= 0.5 * options.seconds:
break
if time < 0.5:
steps = int(
steps * 1.0 / time
) # Integrate enough steps to get a reasonable estimate for how many we'll need.
else:
steps = int(steps * options.seconds / time)
print('Integrated %d steps in %g seconds' % (steps, time))
print('%g ns/day' %
(dt * steps * 86400 / time).value_in_unit(unit.nanoseconds))
def create_openmm_system(sim_openmm, model, anchor):
"""
Create an openmm System() object.
"""
building_directory = os.path.join(model.anchor_rootdir, anchor.directory,
anchor.building_directory)
box_vectors = None
if anchor.amber_params is not None:
prmtop_filename = os.path.join(building_directory,
anchor.amber_params.prmtop_filename)
prmtop = openmm_app.AmberPrmtopFile(prmtop_filename)
assert anchor.amber_params.pdb_coordinates_filename is not None
pdb_coordinates_filename = os.path.join(
building_directory, anchor.amber_params.pdb_coordinates_filename)
positions = openmm_app.PDBFile(pdb_coordinates_filename)
#assert anchor.amber_params.box_vectors is not None
box_vectors = anchor.amber_params.box_vectors
topology = prmtop
elif anchor.forcefield_params is not None:
forcefield_filenames = []
for forcefield_filename in \
anchor.forcefield_params.built_in_forcefield_filenames:
forcefield_filenames.append(forcefield_filename)
for forcefield_filename in \
anchor.forcefield_params.custom_forcefield_filenames:
forcefield_filenames.append(
os.path.join(building_directory, forcefield_filename))
pdb_filename = os.path.join(building_directory,
anchor.forcefield_params.pdb_filename)
pdb = openmm_app.PDBFile(pdb_filename)
forcefield = openmm_app.ForceField(*forcefield_filenames)
box_vectors = anchor.forcefield_params.box_vectors
topology = pdb
positions = pdb
elif anchor.charmm_params is not None:
raise Exception("Charmm systems not yet implemented")
else:
raise Exception("No Amber or Charmm input settings detected.")
#assert box_vectors is not None, "No source of box vectors provided."
nonbonded_method = model.openmm_settings.nonbonded_method.lower()
if nonbonded_method == "pme":
nonbondedMethod = openmm_app.PME
elif nonbonded_method == "nocutoff":
nonbondedMethod = openmm_app.NoCutoff
elif nonbonded_method == "cutoffnonperiodic":
nonbondedMethod = openmm_app.CutoffNonPeriodic
elif nonbonded_method == "cutoffperiodic":
nonbondedMethod = openmm_app.CutoffPeriodic
elif nonbonded_method == "ewald":
nonbondedMethod = openmm_app.Ewald
else:
raise Exception("nonbonded method not found: %s",
model.openmm_settings.nonbonded_method)
if model.openmm_settings.constraints is None:
constraints_str = None
else:
constraints_str = model.openmm_settings.constraints
if constraints_str is None:
constraints = None
elif constraints_str.lower() == "none":
constraints = None
elif constraints_str.lower() == "hbonds":
constraints = openmm_app.HBonds
elif constraints_str.lower() == "allbonds":
constraints = openmm_app.AllBonds
elif constraints_str.lower() == "hangles":
constraints = openmm_app.HAngles
else:
raise Exception("constraints not found: %s",
model.openmm_settings.constraints)
if model.openmm_settings.hydrogenMass:
hydrogenMass = model.openmm_settings.hydrogenMass * openmm.unit.amu
else:
hydrogenMass = model.openmm_settings.hydrogenMass
rigidWater = model.openmm_settings.rigidWater
if anchor.amber_params is not None:
system = prmtop.createSystem(
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=model.openmm_settings.nonbonded_cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass,
rigidWater=rigidWater)
elif anchor.forcefield_params is not None:
system = forcefield.createSystem(
pdb.topology,
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=model.openmm_settings.nonbonded_cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass,
rigidWater=rigidWater)
elif anchor.charmm_params is not None:
raise Exception("Charmm input settings not yet implemented")
else:
print("Settings for Amber or Charmm simulations not found")
return system, topology, positions, box_vectors