bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
torsion_force_constants=torsion_force_constants,
equil_torsion_angles=equil_torsion_angles,
torsion_periodicities=torsion_periodicities,
include_nonbonded_forces=include_nonbonded_forces,
include_bond_forces=include_bond_forces,
include_bond_angle_forces=include_bond_angle_forces,
include_torsion_forces=include_torsion_forces,
constrain_bonds=constrain_bonds,
positions=positions,
)
# Set parameters for definition/evaluation of native contacts
native_structure_contact_distance_cutoff = 1.05 * cgmodel.get_sigma(
0
) # This distance cutoff determines which nonbonded interactions are considered 'native' contacts
native_contact_cutoff_ratio = 1.1 # The distance ratio (in comparison with the distance of a contact in the native structure) below which a nonbonded interaction is considered 'native'
temperature = 400.0 * unit.kelvin
T_list = [temperature.__add__(i * 50.0 * unit.kelvin) for i in range(10)]
for temperature in T_list:
print(
str("Running a simulation with temperature = " +
str(temperature._value)))
output_directory = str("scan_T_output/" + str(temperature._value))
if not os.path.exists(output_directory):
os.mkdir(output_directory)
run_simulation(
total_simulation_time=total_simulation_time,
print_frequency=print_frequency,
output_data=output_data,
)
make_replica_pdb_files(cgmodel.topology, replica_positions)
native_structure = get_native_structure(replica_positions, replica_energies, temperature_list)
random_poses, random_pose_energies = get_decorrelated_samples(
replica_positions, replica_energies, temperature_list
)
# Set parameters for definition/evaluation of native contacts
native_structure_contact_distance_cutoff = 1.05 * cgmodel.get_sigma(
0
) # This distance cutoff determines which nonbonded interactions are considered 'native' contacts
native_contact_cutoff_ratio = 1.1 # The distance ratio (in comparison with the distance of a contact in the native structure) below which a nonbonded interaction is considered 'native'
cutoff_list = [(1.0 + i * 0.01) * cgmodel.get_sigma(0) for i in range(30)]
list_fraction_native_contacts = []
for cutoff in cutoff_list:
# Get the number of nonbonded interactions that will be considered 'native'
# Get the fraction of native contacts for the comparison pose
nonnative_ensemble_Q_list = []
for pose in random_poses:
Q = fraction_native_contacts(
cgmodel,