def ufed_model(
temp=300 * unit.kelvin,
mass=50 * unit.dalton * (unit.nanometer / unit.radians)**2,
Ks=1000 * unit.kilojoules_per_mole / unit.radians**2,
Ts=1500 * unit.kelvin,
limit=180 * unit.degrees,
sigma=18 * unit.degrees,
height=0.0,
frequency=10,
enforce_gridless=False,
):
model = ufedmm.AlanineDipeptideModel()
s_phi = ufedmm.DynamicalVariable('s_phi',
-limit,
limit,
mass,
Ts,
model.phi,
Ks,
sigma=sigma)
s_psi = ufedmm.DynamicalVariable('s_psi',
-limit,
limit,
mass,
Ts,
model.psi,
Ks,
sigma=sigma)
return model, ufedmm.UnifiedFreeEnergyDynamics(
[s_phi, s_psi],
temp,
height,
frequency,
enforce_gridless=enforce_gridless)
def ufed_model():
model = ufedmm.AlanineDipeptideModel()
mass = 50*unit.dalton*(unit.nanometer/unit.radians)**2
Ks = 1000*unit.kilojoules_per_mole/unit.radians**2
Ts = 1500*unit.kelvin
limit = 180*unit.degrees
sigma = 18*unit.degrees
height = 2.0*unit.kilojoules_per_mole
frequency = 10
phi = ufedmm.CollectiveVariable('phi', model.phi, -limit, limit, mass, Ks, Ts, sigma)
psi = ufedmm.CollectiveVariable('psi', model.psi, -limit, limit, mass, Ks, Ts, sigma)
return model, ufedmm.UnifiedFreeEnergyDynamics([phi, psi], 300*unit.kelvin, height, frequency)
temp = 300 * unit.kelvin
gamma = 10 / unit.picoseconds
dt = 2 * unit.femtoseconds
nsteps = 1000000
mass = 30 * unit.dalton * (unit.nanometer / unit.radians)**2
Ks = 1000 * unit.kilojoules_per_mole / unit.radians**2
Ts = 1500 * unit.kelvin
limit = 180 * unit.degrees
sigma = 18 * unit.degrees
height = 2.0 * unit.kilojoules_per_mole
deposition_period = 200
phi = ufedmm.CollectiveVariable('phi', model.phi, -limit, limit, mass, Ks, Ts,
sigma)
psi = ufedmm.CollectiveVariable('psi', model.psi, -limit, limit, mass, Ks, Ts,
sigma)
ufed = ufedmm.UnifiedFreeEnergyDynamics([phi, psi], temp, height,
deposition_period)
ufedmm.serialize(ufed, 'ufed_object.yml')
integrator = ufedmm.GeodesicBAOABIntegrator(temp, gamma, dt)
integrator.setRandomNumberSeed(seed)
platform = openmm.Platform.getPlatformByName(args.platform)
simulation = ufed.simulation(model.topology, model.system, integrator,
platform)
ufed.set_positions(simulation, model.positions)
ufed.set_random_velocities(simulation, seed)
output = ufedmm.MultipleFiles(stdout, 'output.csv')
reporter = ufedmm.StateDataReporter(output,
100,
ufed.driving_force,
step=True,
speed=True)
simulation.reporters.append(reporter)