warmup.promote_parameter('trajectory_interval',
promoted_name='w_trajectory_interval',
default=0,
description='Trajectory saving interval')
warmup.promote_parameter('reporter_interval',
promoted_name='w_reporter_interval',
default=0,
description='Reporter saving interval')
warmup.promote_parameter('outfname',
promoted_name='w_outfname',
default='warmup',
description='Equilibration suffix name')
warmup.promote_parameter('center', promoted_name='center', default=True)
# NPT Equilibration stage
equil = OpenMMnptCube('equil', title='equil')
equil.promote_parameter('time',
promoted_name='eq_psec',
default=20.0,
description='Length of MD run in picoseconds')
equil.promote_parameter('restraints',
promoted_name='eq_restraints',
default="noh ligand",
description='Select mask to apply restraints')
equil.promote_parameter('restraintWt',
promoted_name='eq_restraintWt',
default=0.1,
description='Restraint weight in kcal/(mol A^2')
equil.promote_parameter('trajectory_interval',
promoted_name='eq_trajectory_interval',
default=0,
Outputs:
--------
ofs: Outputs the constant temperature and pressure system
"""
job.classification = [['NPT']]
job.tags = [tag for lists in job.classification for tag in lists]
ifs = OEMolIStreamCube("SystemReader", title="System Reader")
ifs.promote_parameter("data_in",
promoted_name="system",
title='System Input File',
description="System input file")
npt = OpenMMnptCube('npt')
npt.promote_parameter('time',
promoted_name='picosec',
default=10.0,
description='Length of MD run in picoseconds')
npt.promote_parameter('temperature',
promoted_name='temperature',
default=300.0,
description='Selected temperature in K')
npt.promote_parameter('pressure',
promoted_name='pressure',
default=1.0,
description='Selected pressure in atm')
# Restraints
npt.promote_parameter('restraints',
warmup.promote_parameter('reporter_interval',
promoted_name='w_reporter_interval',
default=0,
description='Reporter saving interval')
warmup.promote_parameter('outfname',
promoted_name='w_outfname',
default='warmup',
description='Equilibration suffix name')
# The system is equilibrated at the right pressure and temperature in 3 stages
# The main difference between the stages is related to the restraint force used
# to keep the ligand and protein in their starting positions. A relatively strong force
# is applied in the first stage while a relatively small one is applied in the latter
# NPT Equilibration stage 1
equil1 = OpenMMnptCube('equil1', title='equil1')
equil1.promote_parameter('time',
promoted_name='eq1_psec',
default=100.0,
description='Length of MD run in picoseconds')
equil1.promote_parameter('restraints',
promoted_name='eq1_restraints',
default="noh (ligand or protein)",
description='Select mask to apply restarints')
equil1.promote_parameter('restraintWt',
promoted_name='eq1_restraintWt',
default=2.0,
description='Restraint weight')
equil1.promote_parameter('trajectory_interval',
promoted_name='eq1_trajectory_interval',
default=0,
warmupComplex.promote_parameter('reporter_interval',
promoted_name='w_reporter_interval',
default=0,
description='Reporter saving interval')
warmupComplex.promote_parameter('outfname',
promoted_name='w_outfname',
default='warmup',
description='Equilibration suffix name')
# The system is equilibrated at the right pressure and temperature in 3 stages
# The main difference between the stages is related to the restraint force used
# to keep the ligand and protein in their starting positions. A relatively strong force
# is applied in the first stage while a relatively small one is applied in the latter
# NPT Equilibration stage 1
equil1Complex = OpenMMnptCube('equil1Complex', title='equil1Complex')
equil1Complex.promote_parameter('time',
promoted_name='eq1_psec',
default=20.0,
description='Length of MD run in picoseconds')
equil1Complex.promote_parameter('restraints',
promoted_name='eq1_restraints',
default="noh (ligand or protein)",
description='Select mask to apply restarints')
equil1Complex.promote_parameter('restraintWt',
promoted_name='eq1_restraintWt',
default=2.0,
description='Restraint weight')
equil1Complex.promote_parameter('trajectory_interval',
promoted_name='eq1_trajectory_interval',
default=0,
def setUp(self):
self.cube = OpenMMnptCube('NPT')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
class NPTCubeTester(unittest.TestCase):
"""
Test the OpenMM NPT cube
Example inputs from `openmm_orion/examples/data`
"""
def calculate_VT(self, oe_mol):
# Extract starting MD data from OEMol
mdData = utils.MDData(oe_mol)
structure = mdData.structure
topology = mdData.topology
positions = mdData.positions
velocities = mdData.velocities
box = mdData.box
volume = box[0][0] * box[1][1] * box[2][2]
# OpenMM system
system = structure.createSystem(nonbondedMethod=eval("app.%s" % self.cube.args.nonbondedMethod),
nonbondedCutoff=self.cube.args.nonbondedCutoff * unit.angstroms,
constraints=eval("app.%s" % self.cube.args.constraints))
# OpenMM Integrator
integrator = openmm.LangevinIntegrator(self.cube.args.temperature * unit.kelvin,
1.0 / unit.picoseconds, 0.002 * unit.picoseconds)
# Add Force Barostat to the system
system.addForce(openmm.MonteCarloBarostat(self.cube.args.pressure * unit.atmospheres,
self.cube.args.temperature*unit.kelvin, 25))
# Set Simulation
simulation = app.Simulation(topology, system, integrator)
# Set Positions
simulation.context.setPositions(positions)
# Set Velocities
simulation.context.setVelocities(velocities)
# Set Box dimensions
simulation.context.setPeriodicBoxVectors(box[0], box[1], box[2])
# Collect the OpenMM state energy info
state = simulation.context.getState(getEnergy=True)
# Kinetic Energy
keng = state.getKineticEnergy()
# Calculate system degrees of freedom:
dof = 0
for i in range(system.getNumParticles()):
if system.getParticleMass(i) > 0 * unit.dalton:
dof += 3
dof -= system.getNumConstraints()
if any(type(system.getForce(i)) == openmm.CMMotionRemover for i in range(system.getNumForces())):
dof -= 3
# Calculate the temperature from the equipartition theorem
temperature = ((2*keng)/(dof*unit.MOLAR_GAS_CONSTANT_R))
return volume, temperature
def setUp(self):
self.cube = OpenMMnptCube('NPT')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
def _test_success(self):
print('Testing cube:', self.cube.name)
# Complex file name
complex_fname = utils.get_data_filename('examples', 'data/pP38_lp38a_2x_complex.oeb.gz')
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(complex_fname) as ifs:
oechem.OEReadMolecule(ifs, mol)
# Process the molecules
self.cube.process(mol, self.cube.intake.name)
# Assert that one molecule was emitted on the success port
self.assertEqual(self.runner.outputs['success'].qsize(), 1)
# Assert that zero molecules were emitted on the failure port
self.assertEqual(self.runner.outputs['failure'].qsize(), 0)
outmol = self.runner.outputs["success"].get()
# Calculate final volume and temperature
vol_f, temp_f = self.calculate_VT(outmol)
# Check 3*std volume
# Average volume and its standard deviation (in nm^3) measured along
# one 10ns run for the selected system
avg_volume = 683.6 * (unit.nanometers**3)
std_volume = 1.3
self.assertAlmostEqual(avg_volume/(unit.nanometers**3),
vol_f.in_units_of(unit.nanometers**3)/(unit.nanometers**3),
delta=3*std_volume)
# Check 3*std temperature
# Average temperature and its standard deviation (in K) measured along
# one 10ns run for the selected system
avg_temperature = 300.0 * unit.kelvin
std_temperature = 1.1
self.assertAlmostEqual(avg_temperature/unit.kelvin,
temp_f.in_units_of(unit.kelvin)/unit.kelvin,
delta=3*std_temperature)
@pytest.mark.slow
def test_success(self):
self.cube.args.time = 50.0 # in picoseconds
self._test_success()
def test_failure(self):
pass
def tearDown(self):
self.runner.finalize()
from OpenMMCubes.cubes import OpenMMnptCube
job = WorkFloe("Production Run")
job.description = """
Run an unrestrained NPT simulation at 300K and 1atm
"""
job.classification = [['Simulation']]
job.tags = [tag for lists in job.classification for tag in lists]
ifs = OEMolIStreamCube("SystemReader", title="System Reader")
ifs.promote_parameter("data_in", promoted_name="system", title='System Input File',
description="System input file")
prod = OpenMMnptCube('production')
# Set simulation time
prod.promote_parameter('time', promoted_name='picosec', default=2000)
# Set the temperature in K
prod.promote_parameter('temperature', promoted_name='temperature', default=300.0,
description='Selected temperature in K')
# Set the pressure in atm
prod.promote_parameter('pressure', promoted_name='pressure', default=1.0,
description='Selected pressure in atm')
# Trajectory and logging info frequency intervals
prod.promote_parameter('trajectory_interval', promoted_name='trajectory_interval', default=1000,
description='Trajectory saving interval')