def test_protocol_work_accumulation_waterbox(self):
"""Testing protocol work accumulation for ExternalPerturbationLangevinIntegrator with AlchemicalWaterBox
"""
from simtk.openmm import app
parameter_name = "lambda_electrostatics"
parameter_initial = 1.0
parameter_final = 0.0
platform_names = [
openmm.Platform.getPlatform(index).getName()
for index in range(openmm.Platform.getNumPlatforms())
]
for nonbonded_method in ["CutoffPeriodic", "PME"]:
testsystem = testsystems.AlchemicalWaterBox(
nonbondedMethod=getattr(app, nonbonded_method))
for platform_name in platform_names:
name = "%s %s %s" % (testsystem.name, nonbonded_method,
platform_name)
self.compare_external_protocol_work_accumulation(
testsystem,
parameter_name,
parameter_initial,
parameter_final,
platform_name=platform_name,
name=name,
)
def test_protocol_work_accumulation_waterbox_barostat(self):
"""
Testing protocol work accumulation for ExternalPerturbationLangevinIntegrator with AlchemicalWaterBox
with an active barostat. For brevity, only using CutoffPeriodic as the non-bonded method.
"""
from simtk.openmm import app
parameter_name = "lambda_electrostatics"
parameter_initial = 1.0
parameter_final = 0.0
platform_names = [
openmm.Platform.getPlatform(index).getName()
for index in range(openmm.Platform.getNumPlatforms())
]
nonbonded_method = "CutoffPeriodic"
testsystem = testsystems.AlchemicalWaterBox(
nonbondedMethod=getattr(app, nonbonded_method))
# Adding the barostat with a high frequency
testsystem.system.addForce(
openmm.MonteCarloBarostat(1 * unit.atmospheres, 300 * unit.kelvin,
2))
for platform_name in platform_names:
name = "%s %s %s" % (testsystem.name, nonbonded_method,
platform_name)
self.compare_external_protocol_work_accumulation(
testsystem,
parameter_name,
parameter_initial,
parameter_final,
platform_name=platform_name,
name=name,
)
def generate_example_waterbox_states(temperature=300.0 * unit.kelvin,
pressure=1.0 * unit.atmosphere):
"""
This is a convenience function to generate a CompoundThermodynamicState and SamplerState to use in other tests.
Here, we generate an alchemical water box
"""
#get the water box testsystem
water_ts = testsystems.AlchemicalWaterBox()
system = water_ts.system
positions = water_ts.positions
#construct the openmmtools objects for it
sampler_state = states.SamplerState(
positions, box_vectors=system.getDefaultPeriodicBoxVectors())
thermodynamic_state = states.ThermodynamicState(system,
temperature=temperature,
pressure=pressure)
#make an alchemical state
alchemical_state = alchemy.AlchemicalState.from_system(system)
alchemical_state.set_alchemical_parameters(0.0)
#make a compound thermodynamic state
cpd_thermodynamic_state = states.CompoundThermodynamicState(
thermodynamic_state, [alchemical_state])
return cpd_thermodynamic_state, sampler_state, water_ts.topology
def test_initial_protocol_work(self):
"""
Ensure the protocol work is initially zero and remains zero after a number of integrator steps.
"""
from simtk.openmm import app
parameter_name = 'lambda_electrostatics'
temperature = 298.0 * unit.kelvin
parameter_initial = 1.0
platform_name = 'CPU'
nonbonded_method = 'CutoffPeriodic'
# Create the system
testsystem = testsystems.AlchemicalWaterBox(nonbondedMethod=getattr(app, nonbonded_method))
testsystem.system.addForce(openmm.MonteCarloBarostat(1 * unit.atmospheres, temperature, 2))
context, integrator = self.create_system(testsystem, parameter_name, parameter_initial, temperature, platform_name)
assert (integrator.get_protocol_work(dimensionless=True) == 0)
integrator.step(5)
assert(integrator.get_protocol_work(dimensionless=True) == 0)