def test_explicit_runner_scaler(self): # alanine dipeptide in TIP3P box sys = system.builder.load_amber_system(self.top_path, self.mdcrd_path) sys.temperature_scaler = system.ConstantTemperatureScaler(300.) rest2_scaler = system.GeometricTemperatureScaler(0, 1, 300., 350.) options = system.RunOptions(solvation="explicit") options.rest2_scaler = system.REST2Scaler(300., rest2_scaler) options.timesteps = 20 options.use_rest2 = True runner = OpenMMRunner(sys, options, platform="Reference") runner.prepare_for_timestep(0., 1) pos = sys._coordinates.copy() vel = np.zeros_like(pos) alpha = 0. energy = 0. box_vectors = sys._box_vectors state = system.SystemState(pos, vel, alpha, energy, box_vectors) state = runner.minimize_then_run(state) state = runner.run(state) assert state
def test_implicit_runner_amap(self): p = system.ProteinMoleculeFromSequence("NALA ALA CALA") b = system.SystemBuilder() sys = b.build_system_from_molecules([p]) sys.temperature_scaler = system.ConstantTemperatureScaler(300.) options = system.RunOptions() options.timesteps = 20 options.use_amap = True options.amap_beta_bias = 10 runner = OpenMMRunner(sys, options, platform="Reference") runner.prepare_for_timestep(0., 1) pos = sys._coordinates.copy() vel = np.zeros_like(pos) alpha = 0. energy = 0. box_vectors = np.zeros(3) state = system.SystemState(pos, vel, alpha, energy, box_vectors) state = runner.minimize_then_run(state) state = runner.run(state) assert state
def main(): p = system.ProteinMoleculeFromSequence('NALA ALA CALA') b = system.SystemBuilder() sys = b.build_system_from_molecules([p]) sys.temperature_scaler = system.ConstantTemperatureScaler(300.) options = system.RunOptions() options.timesteps = 10000 options.use_amap = True options.amap_beta_bias = 10 runner = system.OpenMMRunner(sys, options) runner.set_alpha_and_timestep(0., 0) pos = sys._coordinates.copy() vel = numpy.zeros_like(pos) alpha = 0. energy = 0. box_vectors = np.zeros(3) state = system.SystemState(pos, vel, alpha, energy, box_vectors) state = runner.minimize_then_run(state) state = runner.run(state) assert state
def setup_system(): s = system.builder.load_amber_system("system.top", "system.mdcrd") s.temperature_scaler = system.ConstantTemperatureScaler(300.) # create the options options = system.RunOptions(solvation="explicit") options.enable_pme = True options.pme_tolerance = 0.0005 options.enable_pressure_coupling = True options.pressure = 1.0 options.pressure_coupling_update_steps = 25 options.timesteps = 10 options.minimize_steps = 50 # create a store store = vault.DataStore(s.n_atoms, N_REPLICAS, s.get_pdb_writer(), block_size=BLOCK_SIZE) store.initialize(mode="w") store.save_system(s) store.save_run_options(options) # create and store the remd_runner l = ladder.NearestNeighborLadder(n_trials=48 * 48) a = adaptor.NullAdaptor(N_REPLICAS) remd_runner = master_runner.MasterReplicaExchangeRunner(N_REPLICAS, max_steps=N_STEPS, ladder=l, adaptor=a) store.save_remd_runner(remd_runner) # create and store the communicator c = comm.MPICommunicator(s.n_atoms, N_REPLICAS) store.save_communicator(c) # create and save the initial states states = [gen_state(s, i) for i in range(N_REPLICAS)] store.save_states(states, 0) # save data_store store.save_data_store() return s.n_atoms
def test_runner(self): p = system.ProteinMoleculeFromSequence('NALA ALA CALA') b = system.SystemBuilder() sys = b.build_system_from_molecules([p]) sys.temperature_scaler = system.ConstantTemperatureScaler(300.) options = system.RunOptions() options.timesteps = 10000 runner = system.OpenMMRunner(sys, options) runner.set_alpha_and_timestep(0., 1) pos = sys._coordinates.copy() vel = numpy.zeros_like(pos) alpha = 0. energy = 0. state = system.SystemState(pos, vel, alpha, energy) state = runner.minimize_then_run(state) state = runner.run(state) assert state