[Questions] How to report to stdout while running ReplicaExchangeSampler

[4doom4]

I am using MultiStateReporter ("file.nc", checkpoint_interval=interval) as the storage in a simulation from ReplicaExchangeSampler. This works to have the states as netcdf once the simulation is done. Is there a way to attach multiple reports to the simulation like in native openmm to report to stdout information on the progress of the simulation? I saw https://openmmtools.readthedocs.io/en/stable/devtutorial.html#id18 but I am not sure how to use this.

Thanks.

[ijpulidos]

Some progress of the simulation should already be given in stdout by default. Can you share the code that you are using that's not reporting anything on stdout?

[4doom4]

I basically followed the REST2 protocol from here: https://openmm.github.io/openmm-cookbook/latest/notebooks/tutorials/Running_a_REST_simulation.html

The relevant part of the script:

print("Configuring REST2 protocol...")
# Set temperatures for each thermodynamic state
n_replicas = 16  # Number of temperature replicas
T_min = 300 * kelvin  # Minimum temperature (i.e., temperature of desired distribution)
T_max = 600 * kelvin  # Maximum temperature
temperatures = [T_min + (T_max - T_min) * (math.exp(float(i) / float(n_replicas-1)) - 1.0) / (math.e - 1.0)
                for i in range(n_replicas)]


# Create reference thermodynamic state
rest_state = RESTState.from_system(rest_system)
thermostate = ThermodynamicState(rest_system, temperature=T_min)
compound_thermodynamic_state = CompoundThermodynamicState(thermostate, composable_states=[rest_state])


# Create thermodynamic states
sampler_state =  SamplerState(coord.positions, box_vectors=rest_system.getDefaultPeriodicBoxVectors())
beta_0 = 1/(kB*T_min)
thermodynamic_state_list = []
sampler_state_list = []
for temperature in temperatures:
    # Create a thermodynamic state with REST interactions scaled to the given temperature
    beta_m = 1/(kB*temperature)
    compound_thermodynamic_state_copy = copy.deepcopy(compound_thermodynamic_state)
    compound_thermodynamic_state_copy.set_rest_parameters(beta_m, beta_0)
    thermodynamic_state_list.append(compound_thermodynamic_state_copy)

    # Generate a sampler_state with minimized positions
    context, integrator = cache.global_context_cache.get_context(compound_thermodynamic_state_copy)
    sampler_state.apply_to_context(context, ignore_velocities=True)
    openmm.LocalEnergyMinimizer.minimize(context)
    sampler_state.update_from_context(context)
    sampler_state_list.append(copy.deepcopy(sampler_state))


# Set up sampler
swap_attempts = 500
move = mcmc.LangevinDynamicsMove(timestep=0.002*picoseconds, n_steps=1000) # each move is 2 ps
simulation = ReplicaExchangeSampler(mcmc_moves=move, number_of_iterations=swap_attempts)

# Run repex
start, start_time = timer()
print(f"Start REST2 protocol at {start_time}...")
reporter = multistate.MultiStateReporter(f"{prefix}_rest2.nc", checkpoint_interval=5)

simulation.create(thermodynamic_states=thermodynamic_state_list,
                  sampler_states=sampler_state_list,
                  storage=reporter)

simulation.run()

end, end_time = timer()
print(f"REST2 protocol completed at {end_time}. Elapsed time: {end - start:.2f} seconds")