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_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, test=True)
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 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, test=True)
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