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))