# Load the configuration
configuration = nlread("equilibrated_teflon.hdf5")[0]

# Create and set the calculator
builder = OPLSPotentialBuilder()
calculator = SoftMatterCalculator(
    builder, use_lennard_jones_pme=True, assign_atom_types=True
)
configuration.setCalculator(calculator)

# Set the simulation
atomic_constraints = [FixCenterOfMass()]
method = NVTAndersen(
    time_step=2*fs,
    initial_velocity=ConfigurationVelocities(),
    reservoir_temperature=400*Kelvin,
)
simulation = SoftMatterDynamicsSimulation(
    configuration, method, atomic_constraints=atomic_constraints
)
simulation.setLogging(1000)
simulation.setTrajectory(10000, "teflon_trajectory.hdf5")

# Run the simulation
simulation.simulate(100000)