def hmc_inner(system, positions, params):
groups = set_respa(system, params["respa"])
integrator = hmc_integrators.GHMCRESPA(temperature, params["steps_per_hmc"], params["timestep"] * u.femtoseconds, collision_rate, groups)
context = mm.Context(system, integrator)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(n_steps)
d = integrator.summary
d.update(params)
print(pd.Series(d))
print("**************************** %f" % integrator.effective_ns_per_day)
return d
integrator = hmc_integrators.GHMC2(temperature, 50, timestep)
integrator.getNumComputations()
context = mm.Context(system, integrator)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(1)
%timeit integrator.step(4)
for k in range(integrator.getNumComputations()):
print(integrator.getComputationStep(k))
groups = [(0, 1)]
integrator = hmc_integrators.GHMCRESPA(temperature, 50, timestep, collision_rate, groups)
integrator.getNumComputations()
context = mm.Context(system, integrator)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(1)
%timeit integrator.step(4)
for k in range(integrator.getNumComputations()):
print(integrator.getComputationStep(k))
integrator = hmc_integrators.XHMCIntegrator(temperature,
steps_per_hmc=10,
timestep=timestep,
collision_rate=1.0 / u.picoseconds,
extra_chances=5)
context = mm.Context(system, integrator)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
data["xhmc1"] = pd.DataFrame(sample(context, n_iter=n_iter, n_steps=1))
groups = [(0, 2), (1, 1)]
hmc_integrators.guess_force_groups(system, nonbonded=0, fft=1, others=0)
integrator = hmc_integrators.GHMCRESPA(temperature,
steps_per_hmc=10,
timestep=timestep,
collision_rate=1.0 / u.picoseconds,
groups=groups)
context = mm.Context(system, integrator)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
data["ghmcrespa1"] = pd.DataFrame(sample(context, n_iter=n_iter, n_steps=1))
groups = [(0, 2), (1, 1)]
hmc_integrators.guess_force_groups(system, nonbonded=0, fft=1, others=0)
integrator = hmc_integrators.XHMCRESPAIntegrator(temperature,
steps_per_hmc=10,
timestep=timestep,
collision_rate=1.0 /
u.picoseconds,
cutoff = 1.0 * u.nanometers
hydrogenMass = 1.0 * u.amu
testsystem = testsystems.DHFRExplicit(hydrogenMass=hydrogenMass, cutoff=cutoff)
system, positions = testsystem.system, testsystem.positions
positions = lb_loader.pre_equil(system, positions, temperature)
platform_properties = dict(CudaPrecision="mixed")
steps_per_hmc = 17
timestep = 1.5 * u.femtoseconds
hmc_integrators.guess_force_groups(system, nonbonded=1, fft=1, others=0)
factor = 1
groups = [(0, 2), (1, 1)]
integrator = hmc_integrators.GHMCRESPA(temperature, steps_per_hmc, timestep,
collision_rate, groups)
context = mm.Context(system, integrator, platform, platform_properties)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(1)
integrator.step(n_steps)
integrator.vstep(5)
platform_properties = dict(CudaPrecision="single")
steps_per_hmc = 17
timestep = 1.5 * u.femtoseconds
hmc_integrators.guess_force_groups(system, nonbonded=1, fft=1, others=0)
factor = 1
groups = [(0, 2), (1, 1)]