def test_hmc(timestep, steps_per_hmc):
timestep = timestep * u.femtoseconds
integrator = hmc_integrators.HMCIntegrator(temperature, steps_per_hmc, timestep)
context = mm.Context(system, integrator, platform)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(n_steps)
return integrator.acceptance_rate
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
precision = "mixed"
sysname = "switchedaccuratewater"
system, positions, groups, temperature, timestep, langevin_timestep, testsystem = lb_loader.load(
sysname)
integrator = hmc_integrators.HMCIntegrator(temperature,
steps_per_hmc=25,
timestep=timestep)
context = lb_loader.build(system, integrator, positions, temperature)
mm.LocalEnergyMinimizer.minimize(context)
integrator.step(40000)
positions = context.getState(getPositions=True).getPositions()
print(integrator.acceptance_rate)
collision_rate = 1.0 / u.picoseconds
n_steps = 25
Neff_cutoff = 1E5
itype = "HMCIntegrator"
integrator = hmc_integrators.HMCIntegrator(temperature,
steps_per_hmc=25,
return xyz, n
n = 4 * (2**3)
xyz, box = build_lattice(n)
traj = generate_dummy_trajectory(xyz, box)
traj.save("./out.pdb")
len(xyz)
x = np.linspace(0, 16, 5000)
y = np.array([f(xi) for xi in x])
plot(x, y)
testsystem = LennardJonesFluid(nparticles=1000, hcp=True)
system, positions = testsystem.system, testsystem.positions
temperature = 25 * u.kelvin
integrator = hmc_integrators.HMCIntegrator(temperature,
steps_per_hmc=25,
timestep=1.0 * u.femtoseconds)
context = lb_loader.build(system, integrator, positions, temperature)
context.getState(getEnergies=True).getPotentialEnergy()
mm.LocalEnergyMinimizer.minimize(context)
context.getState(getEnergies=True).getPotentialEnergy()
integrator.step(400)
context.getState(getEnergies=True).getPotentialEnergy()