def test_generateSimFromStruct(self):
print('Generating Simulation from parmed.Structure')
integrator = openmm.LangevinIntegrator(100 * unit.kelvin, 1,
0.002 * unit.picoseconds)
simulation = SimulationFactory.generateSimFromStruct(
self.structure, self.system, integrator)
#Check that we've made a Simulation object
self.assertIsInstance(simulation, app.Simulation)
state = simulation.context.getState(getPositions=True)
positions = state.getPositions(asNumpy=True) / unit.nanometers
box_vectors = state.getPeriodicBoxVectors(
asNumpy=True) / unit.nanometers
struct_box = np.array(
self.structure.box_vectors.value_in_unit(unit.nanometers))
struct_pos = np.array(
self.structure.positions.value_in_unit(unit.nanometers))
#Check that the box_vectors/positions in the Simulation
# have been set from the parmed.Structure
np.testing.assert_array_almost_equal(positions, struct_pos)
np.testing.assert_array_equal(box_vectors, struct_box)
print('Attaching Reporter')
reporters = [app.StateDataReporter('test.log', 5)]
self.assertEqual(len(simulation.reporters), 0)
simulation = SimulationFactory.attachReporters(simulation, reporters)
self.assertEqual(len(simulation.reporters), 1)
os.remove('test.log')
def test_generateSimFromStruct(self, structure, system, tmpdir):
print('Generating Simulation from parmed.Structure')
integrator = openmm.LangevinIntegrator(100 * unit.kelvin, 1, 0.002 * unit.picoseconds)
simulation = SimulationFactory.generateSimFromStruct(structure, system, integrator)
#Check that we've made a Simulation object
assert isinstance(simulation, app.Simulation)
state = simulation.context.getState(getPositions=True)
positions = state.getPositions(asNumpy=True) / unit.nanometers
box_vectors = state.getPeriodicBoxVectors(asNumpy=True) / unit.nanometers
struct_box = np.array(structure.box_vectors.value_in_unit(unit.nanometers))
struct_pos = np.array(structure.positions.value_in_unit(unit.nanometers))
#Check that the box_vectors/positions in the Simulation
# have been set from the parmed.Structure
np.testing.assert_array_almost_equal(positions, struct_pos)
np.testing.assert_array_equal(box_vectors, struct_box)
print('Attaching Reporter')
reporters = [app.StateDataReporter(tmpdir.join('test.log'), 5)]
assert len(simulation.reporters) == 0
simulation = SimulationFactory.attachReporters(simulation, reporters)
assert len(simulation.reporters) == 1
def runEthyleneTest(N):
filename = 'ethylene-test_%s' % N
print('Running %s...' % filename)
seed = np.random.randint(low=1, high=5000)
#print('Seed', seed)
# filename = 'ethylene-test_%s' % N
# print(filename)
# Set Simulation parameters
sim_cfg = {
'platform': 'CPU',
'nprop': 1,
'propLambda': 0.3,
'dt': 1 * unit.femtoseconds,
'friction': 1 / unit.picoseconds,
'temperature': 200 * unit.kelvin,
'nIter': 100,
'nstepsMD': 20,
'nstepsNC': 20,
'propSteps': 20,
'moveStep': 10
}
totalSteps = int(sim_cfg['nIter'] * sim_cfg['nstepsMD'])
reportInterval = 5
alchemical_atoms = [2, 3, 4, 5, 6, 7]
alchemical_functions = {
'lambda_sterics':
'min(1, (1/0.3)*abs(lambda-0.5))',
'lambda_electrostatics':
'step(0.2-lambda) - 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)'
}
md_reporters = {'traj_netcdf': {'reportInterval': reportInterval}}
# Load a Parmed Structure for the Topology and create our openmm.Simulation
structure_pdb = utils.get_data_filename(
'blues', 'tests/data/ethylene_structure.pdb')
structure = parmed.load_file(structure_pdb)
# Initialize our move proposal class
rot_move = RandomLigandRotationMove(structure, 'LIG')
mover = MoveEngine(rot_move)
# Load our OpenMM System and create Integrator
system_xml = utils.get_data_filename('blues',
'tests/data/ethylene_system.xml')
with open(system_xml, 'r') as infile:
xml = infile.read()
system = openmm.XmlSerializer.deserialize(xml)
integrator = openmm.LangevinIntegrator(sim_cfg['temperature'],
sim_cfg['friction'], sim_cfg['dt'])
integrator.setRandomNumberSeed(seed)
alch_integrator = openmm.LangevinIntegrator(sim_cfg['temperature'],
sim_cfg['friction'],
sim_cfg['dt'])
alch_integrator.setRandomNumberSeed(seed)
alch_system = SystemFactory.generateAlchSystem(system, alchemical_atoms)
ncmc_integrator = AlchemicalExternalLangevinIntegrator(
nsteps_neq=sim_cfg['nstepsNC'],
alchemical_functions=alchemical_functions,
splitting="H V R O R V H",
temperature=sim_cfg['temperature'],
timestep=sim_cfg['dt'])
# ncmc_integrator.setRandomNumberSeed(seed)
# Pack our systems into a single object
systems = SystemFactory(structure, alchemical_atoms)
systems.md = system
systems.alch = alch_system
# Make our reporters
md_reporter_cfg = ReporterConfig(filename, md_reporters)
md_reporters_list = md_reporter_cfg.makeReporters()
# Pack our simulations into a single object
simulations = SimulationFactory(systems, mover)
simulations.md = SimulationFactory.generateSimFromStruct(
structure, system, integrator, 'CPU')
simulations.md = SimulationFactory.attachReporters(simulations.md,
md_reporters_list)
simulations.alch = SimulationFactory.generateSimFromStruct(
structure, system, alch_integrator, 'CPU')
simulations.ncmc = SimulationFactory.generateSimFromStruct(
structure, alch_system, ncmc_integrator, 'CPU')
ethylene_sim = BLUESSimulation(simulations, sim_cfg)
ethylene_sim.run()
