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