broken_hmc.py

run_hmc.py

import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import integrators, testsystems

temperature = 300 * u.kelvin

testsystem = testsystems.WaterBox()

integrator = mm.LangevinIntegrator(temperature, 1.0 / u.picoseconds, 0.25 * u.femtoseconds)

context = mm.Context(testsystem.system, integrator)
context.setPositions(testsystem.positions)
context.setVelocitiesToTemperature(temperature)


positions = context.getState(getPositions=True).getPositions()

timestep = 10.0 * u.femtoseconds

integrator = integrators.HMCIntegrator(temperature, nsteps=10, timestep=timestep)

context = mm.Context(testsystem.system, integrator)
context.setPositions(positions)
context.setVelocitiesToTemperature(temperature)

integrator.step(10)