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_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 gen_state(s, index):
pos = s._coordinates
box_vectors = s._box_vectors
vel = np.zeros_like(pos)
alpha = index / (N_REPLICAS - 1.0)
energy = 0
return system.SystemState(pos, vel, alpha, energy, box_vectors)
def gen_state(s):
pos = s._coordinates
vel = np.zeros_like(pos)
box_vectors = [0., 0., 0.]
alpha = 0
energy = 0
return system.SystemState(pos, vel, alpha, energy, box_vectors)
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 gen_state(s, index):
pos = s._coordinates
pos = pos - np.mean(pos, axis=0)
vel = np.zeros_like(pos)
alpha = index / (N_REPLICAS - 1.0)
energy = 0
return system.SystemState(pos, vel, alpha, energy)
def gen_state(s, index):
pos = s._coordinates
pos = pos - np.mean(pos, axis=0)
vel = np.zeros_like(pos)
alpha = index / (N_REPLICAS - 1.0)
s._box_vectors=np.array([0.,0.,0.])
energy = 0
return system.SystemState(pos, vel, alpha, energy,s._box_vectors)
def gen_state(s, index):
pos = s._coordinates
vel = np.zeros_like(pos)
try:
alpha = index / (N_REPLICAS - 1.0)
except:
alpha = 0
energy = 0
return system.SystemState(pos, vel, alpha, energy)
def gen_state_templates(index, templates):
n_templates = len(templates)
# print index,n_templates,index%n_templates
a = system.ProteinMoleculeFromPdbFile(templates[index % n_templates])
b = system.SystemBuilder(forcefield="ff14sbside")
c = b.build_system_from_molecules([a])
pos = c._coordinates
vel = np.zeros_like(pos)
alpha = index / (N_REPLICAS - 1.0)
energy = 0
return system.SystemState(pos, vel, alpha, energy, [999, 999, 999])
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
def gen_state(index, n_atoms):
pos = index * np.ones((n_atoms, 3))
vel = index * np.ones((n_atoms, 3))
energy = index
lam = index / 100.
return system.SystemState(pos, vel, lam, energy, np.zeros(3))
