def main():
# create the system
p = system.SubSystemFromSequence("NALA ALA CALA")
b = system.SystemBuilder()
s = b.build_system([p])
with open("tri_ala.top", "w") as outfile:
outfile.write(s._top_string)
def setup_system():
# get the sequence
sequence = "AAAAAAAAAAAAAAAA"
sequence = parse.get_sequence_from_AA1(contents=sequence)
# create the system
p = system.SubSystemFromSequence(sequence)
b = system.SystemBuilder()
s = b.build_system([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()
# 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 = leader.LeaderReplicaExchangeRunner(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