def test_implicit_runner_amap(self):
p = subsystem.SubSystemFromSequence("NALA ALA CALA")
b = builder.SystemBuilder()
sys = b.build_system([p])
sys.temperature_scaler = temperature.ConstantTemperatureScaler(300.0 * u.kelvin)
opt = options.RunOptions()
opt.timesteps = 20
opt.use_amap = True
opt.amap_beta_bias = 10
runner = openmm_runner.OpenMMRunner(sys, opt, platform="Reference")
runner.prepare_for_timestep(sys.get_state_template(), 0.0, 1)
pos = sys._coordinates.copy()
vel = np.zeros_like(pos)
alpha = 0.0
energy = 0.0
box_vectors = np.zeros(3)
s = state.SystemState(pos, vel, alpha, energy, box_vectors)
s = runner.minimize_then_run(s)
s = runner.run(s)
assert s
def test_explicit_runner_scaler(self):
p = subsystem.SubSystemFromSequence("NALA ALA CALA")
b = builder.SystemBuilder(explicit_solvent=True)
sys = b.build_system([p])
sys.temperature_scaler = temperature.ConstantTemperatureScaler(300.0 * u.kelvin)
rest2_scaler = temperature.GeometricTemperatureScaler(
0, 1, 300.0 * u.kelvin, 350.0 * u.kelvin
)
opt = options.RunOptions(solvation="explicit")
opt.rest2_scaler = temperature.REST2Scaler(300.0 * u.kelvin, rest2_scaler)
opt.minimize_steps = 100
opt.timesteps = 2
opt.use_rest2 = True
runner = openmm_runner.OpenMMRunner(sys, opt, platform="Reference")
runner.prepare_for_timestep(sys.get_state_template(), 0.0, 1)
pos = sys._coordinates.copy()
vel = np.zeros_like(pos)
alpha = 0.0
energy = 0.0
box_vectors = sys._box_vectors
s = state.SystemState(pos, vel, alpha, energy, box_vectors)
s = runner.minimize_then_run(s)
s = runner.run(s)
assert s
def test_raises_when_system_has_no_temperature_scaler(self):
self.system.temperature_scaler = None
with self.assertRaises(RuntimeError):
openmm_runner.OpenMMRunner(self.system, options.RunOptions())