total_steps = round(total_simulation_time.__div__(simulation_time_step))
# Yank (replica exchange) simulation settings
output_data = str(str(top_directory) + "/output.nc")
number_replicas = 30
min_temp = 10.0 * unit.kelvin
max_temp = 200.0 * unit.kelvin
temperature_list = get_temperature_list(min_temp, max_temp, number_replicas)
print("Using " + str(len(temperature_list)) + " replicas.")
cgmodel = CGModel(positions=native_structure)
model_angle_list = cgmodel.bond_angle_list
angle_list = []
for angle in model_angle_list:
if all([cgmodel.get_particle_type(i) == "backbone" for i in angle]):
angle_list.append(angle)
bond_angle_list = []
bin_counts_list = []
bond_angle_force_constant_list = [
unit.Quantity((0.001 * 10**i),
unit.kilocalorie_per_mole / unit.radian / unit.radian)
for i in range(grid_size)
]
for constant in bond_angle_force_constant_list:
bond_angle_force_constants = {'bb_bb_bb_angle_k': constant}
cgmodel = CGModel(positions=native_structure,
bond_angle_force_constants=bond_angle_force_constants)
total_steps = round(total_simulation_time.__div__(simulation_time_step))
# Yank (replica exchange) simulation settings
output_data = str(str(top_directory) + "/output.nc")
number_replicas = 30
min_temp = 10.0 * unit.kelvin
max_temp = 200.0 * unit.kelvin
temperature_list = get_temperature_list(min_temp, max_temp, number_replicas)
print("Using " + str(len(temperature_list)) + " replicas.")
cgmodel = CGModel()
model_torsion_list = cgmodel.torsion_list
torsion_list = []
for torsion in model_torsion_list:
if all([cgmodel.get_particle_type(i) == "backbone" for i in torsion]):
torsion_list.append(torsion)
torsions_list = []
bin_counts_list = []
torsion_force_constant_list = [0.001 * 10**i for i in range(grid_size)]
for constant in torsion_force_constant_list:
torsion_force_constants = {'bb_bb_bb_bb_torsion_k': constant}
cgmodel = CGModel(torsion_force_constants=torsion_force_constants)
output_data = str(
str(top_directory) + "/" + str(round(constant, 3)) + ".nc")
if not os.path.exists(output_data):
replica_energies, replica_positions, replica_states = run_replica_exchange(
cgmodel.topology,
