def setup_system():
# get the sequence
sequence = "AAAAAAAAAAAAAAAA"
sequence = parse.get_sequence_from_AA1(contents=sequence)
# create the system
p = system.ProteinMoleculeFromSequence(sequence)
b = system.SystemBuilder()
s = b.build_system_from_molecules([p])
s.temperature_scaler = system.LinearTemperatureScaler(0, 1, 300, 310)
rest_scaler = s.restraints.create_scaler("nonlinear",
alpha_min=0,
alpha_max=1,
factor=4.0)
secondary = "H" * 16
secondary_restraints = parse.get_secondary_structure_restraints(
system=s, scaler=rest_scaler, contents=secondary)
s.restraints.add_selectively_active_collection(secondary_restraints,
len(secondary_restraints))
# create the options
options = system.RunOptions()
options.use_big_timestep = True
# create a store
store = vault.DataStore(s.n_atoms,
N_REPLICAS,
s.get_pdb_writer(),
block_size=BACKUP_FREQ)
store.initialize(mode="w")
store.save_system(s)
store.save_run_options(options)
# create and store the remd_runner
l = ladder.NearestNeighborLadder(n_trials=1)
policy = adaptor.AdaptationPolicy(1.0, 50, 100)
a = adaptor.EqualAcceptanceAdaptor(n_replicas=N_REPLICAS,
adaptation_policy=policy)
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) for i in range(N_REPLICAS)]
states[1].alpha = 1.0
store.save_states(states, 0)
# save data_store
store.save_data_store()
return s.n_atoms
def setup_system():
# get the sequence
sequence = 'AAAAAAAAAAAAAAAA'
sequence = parse.get_sequence_from_AA1(contents=sequence)
# create the system
p = system.ProteinMoleculeFromSequence(sequence)
b = system.SystemBuilder()
s = b.build_system_from_molecules([p])
s.temperature_scaler = system.LinearTemperatureScaler(0, 1, 300, 310)
rest_scaler = s.restraints.create_scaler('nonlinear', alpha_min=0, alpha_max=1, factor=4.0)
secondary = 'H'*16
secondary_restraints = parse.get_secondary_structure_restraints(system=s, scaler=rest_scaler,
contents=secondary)
s.restraints.add_selectively_active_collection(secondary_restraints, len(secondary_restraints))
# create com restraint
com = s.restraints.create_restraint('com', rest_scaler, ramp=None,
group1=[(1, 'CA')],
group2=[(3, 'CA')],
weights1=None,
weights2=None,
dims='xyz',
force_const=100.,
distance=0.5)
s.restraints.add_as_always_active(com)
# create absolute com restraint
com = s.restraints.create_restraint('abs_com', rest_scaler, ramp=None,
group=[(1, 'CA')],
weights=None,
dims='xyz',
force_const=1.,
position=[0., 0., 0.])
s.restraints.add_as_always_active(com)
# create the options
options = system.RunOptions()
# create a store
store = vault.DataStore(s.n_atoms, N_REPLICAS, s.get_pdb_writer(), block_size=BACKUP_FREQ)
store.initialize(mode='w')
store.save_system(s)
store.save_run_options(options)
# create and store the remd_runner
l = ladder.NearestNeighborLadder(n_trials=1)
policy = adaptor.AdaptationPolicy(1.0, 50, 100)
a = adaptor.EqualAcceptanceAdaptor(n_replicas=N_REPLICAS, adaptation_policy=policy)
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) for i in range(N_REPLICAS)]
states[1].alpha = 1.0
store.save_states(states, 0)
# save data_store
store.save_data_store()
return s.n_atoms
