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

# Create the soft matter calculator
builder = OPLSPotentialBuilder()
calculator = SoftMatterCalculator(builder)
configuration.setCalculator(calculator)

# Create simulation
method = NVEDynamics(initial_velocity=ConfigurationVelocities())
simulation = SoftMatterDynamicsSimulation(configuration, method)
simulation.setLogging(1000)
simulation.setTrajectory(10000, "pp_trajectory.hdf5")

# Run the simulation
simulation.simulate(100000)