"sigmas": sigmas,
}
monomer_types = [A, B]
sequence = [A, A, A, B, A, A, A, B, A, A, A, B]
polymer_length = len(sequence)
cgmodel = CGModel(
polymer_length=polymer_length,
bond_force_constants=bond_force_constants,
bond_angle_force_constants=bond_angle_force_constants,
torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
equil_torsion_angles=equil_torsion_angles,
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,
heteropolymer=True,
monomer_types=monomer_types,
sequence=sequence,
)
if not os.path.exists(output_data):
replica_energies, replica_positions, replica_states = run_replica_exchange(
cgmodel.topology,
cgmodel.system,
cgmodel.positions,
temperature_list=temperature_list,
simulation_time_step=simulation_time_step,
for i in range(sigma_increments)
]
df_ij_list = []
ddf_ij_list = []
Delta_u_list = []
dDelta_u_list = []
Delta_s_list = []
dDelta_s_list = []
C_v_list = []
dC_v_list = []
for sigma in sigma_list:
output_data = str(str(top_directory) + "/rep_ex_" + str(sigma) + ".nc")
sigmas = {"bb_bb_sigma": sigma, "bb_sc_sigma": sigma, "sc_sc_sigma": sigma}
cgmodel = CGModel(sigmas=sigmas)
if not os.path.exists(output_data):
print(
"Performing simulations and free energy analysis for a coarse grained model"
)
print("with sigma values of " + str(sigma))
replica_energies, replica_positions, replica_states = run_replica_exchange(
cgmodel.topology,
cgmodel.system,
cgmodel.positions,
temperature_list=temperature_list,
simulation_time_step=simulation_time_step,
total_simulation_time=total_simulation_time,
print_frequency=print_frequency,
output_data=output_data,
)
torsion_periodicities = {"bb_bb_bb_bb_period": 1} # ,'sc_bb_bb_sc_period': 2}
# Initiate cgmodel using positions from local file
positions = PDBFile("init.pdb").getPositions()
# Build a coarse grained model using the positions for the initial structure
cgmodel = CGModel(
polymer_length=polymer_length,
backbone_lengths=backbone_lengths,
sidechain_lengths=sidechain_lengths,
sidechain_positions=sidechain_positions,
masses=masses,
sigmas=sigmas,
epsilons=epsilons,
bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
torsion_force_constants=torsion_force_constants,
torsion_phase_angles=torsion_phase_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,
)
if os.path.exists(output_data):
# Search for existing data, and read it if possible
replica_energies, replica_positions, replica_states = read_replica_exchange_data(
system=cgmodel.system,
topology=cgmodel.topology,
"bb_bb_bb_sc_torsion_periodicity": 3
}
# Get initial positions from local file
positions = PDBFile("helix.pdb").getPositions()
# Build a coarse grained model
cgmodel = CGModel(
particle_type_list=[bb, sc],
bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
bond_angle_force_constants=bond_angle_force_constants,
torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
torsion_phase_angles=torsion_phase_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,
sequence=sequence,
positions=positions,
monomer_types=[A],
)
# store the cg model so that we can do various analyses.
cgmodel.export("stored_cgmodel.pkl")
if not os.path.exists(output_data) or overwrite_files == True:
run_replica_exchange(
cgmodel.topology,
simulation_time_step = 5.0 * unit.femtosecond
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 = 20
min_temp = 50.0 * unit.kelvin
max_temp = 300.0 * unit.kelvin
temperature_list = get_temperature_list(min_temp, max_temp, number_replicas)
print("Using " + str(len(temperature_list)) + " replicas.")
if total_steps > 10000:
exchange_attempts = round(total_steps / 1000)
else:
exchange_attempts = 10
cgmodel = CGModel()
if not os.path.exists(output_data):
replica_energies, replica_positions, replica_states = run_replica_exchange(
cgmodel.topology,
cgmodel.system,
cgmodel.positions,
temperature_list=temperature_list,
simulation_time_step=simulation_time_step,
total_simulation_time=total_simulation_time,
print_frequency=print_frequency,
output_data=output_data,
)
make_replica_pdb_files(cgmodel.topology, replica_positions)
else:
replica_energies, replica_positions, replica_states = read_replica_exchange_data(
def test_sums_periodic_torsions_5():
# Test cg_model with sums of periodic torsions - test 5
# Two periodic torsion terms, parameters input as quantities with list values
# Parameters are applied to all torsion types using the default input method
# Coarse grained model settings
include_bond_forces = True
include_bond_angle_forces = True
include_nonbonded_forces = True
include_torsion_forces = True
constrain_bonds = False
# Bond definitions
bond_length = 1.5 * unit.angstrom
bond_lengths = {
"bb_bb_bond_length": bond_length,
"bb_sc_bond_length": bond_length,
"sc_sc_bond_length": bond_length,
}
bond_force_constant = 1000 * unit.kilojoule_per_mole / unit.nanometer / unit.nanometer
bond_force_constants = {
"bb_bb_bond_force_constant": bond_force_constant,
"bb_sc_bond_force_constant": bond_force_constant,
"sc_sc_bond_force_constant": bond_force_constant,
}
# Particle definitions
mass = 100.0 * unit.amu
r_min = 1.5 * bond_length # Lennard-Jones potential r_min
# Factor of /(2.0**(1/6)) is applied to convert r_min to sigma
sigma = r_min / (2.0**(1.0 / 6.0))
epsilon = 0.5 * unit.kilojoule_per_mole
bb = {
"particle_type_name": "bb",
"sigma": sigma,
"epsilon": epsilon,
"mass": mass
}
sc = {
"particle_type_name": "sc",
"sigma": sigma,
"epsilon": epsilon,
"mass": mass
}
# Bond angle definitions
bond_angle_force_constant = 100 * unit.kilojoule_per_mole / unit.radian / unit.radian
bond_angle_force_constants = {
"bb_bb_bb_bond_angle_force_constant": bond_angle_force_constant,
"bb_bb_sc_bond_angle_force_constant": bond_angle_force_constant,
}
# OpenMM requires angle definitions in units of radians
bb_bb_bb_equil_bond_angle = 120.0 * unit.degrees
bb_bb_sc_equil_bond_angle = 120.0 * unit.degrees
equil_bond_angles = {
"bb_bb_bb_equil_bond_angle": bb_bb_bb_equil_bond_angle,
"bb_bb_sc_equil_bond_angle": bb_bb_sc_equil_bond_angle,
}
# Torsion angle definitions
torsion_force_constants = {
"default_torsion_force_constant": [5, 10] * unit.kilojoule_per_mole,
}
torsion_phase_angles = {
"default_torsion_phase_angle": [0, 180] * unit.degrees,
}
torsion_periodicities = {
"default_torsion_periodicity": [1, 3],
}
# Monomer definitions
A = {
"monomer_name": "A",
"particle_sequence": [bb, sc],
"bond_list": [[0, 1]],
"start": 0,
"end": 0,
}
sequence = 24 * [A]
pdb_path = os.path.join(data_path, "24mer_1b1s_initial_structure.pdb")
positions = PDBFile(pdb_path).getPositions()
# Build a coarse grained model
cgmodel = CGModel(
particle_type_list=[bb, sc],
bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
bond_angle_force_constants=bond_angle_force_constants,
torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
torsion_phase_angles=torsion_phase_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,
sequence=sequence,
monomer_types=[A],
)
# Check the number of periodic torsions terms:
n_torsion_forces = cgmodel.system.getForces()[3].getNumTorsions()
assert n_torsion_forces == 176
def create_cgmodel():
# Coarse grained model settings
include_bond_forces = True
include_bond_angle_forces = True
include_nonbonded_forces = True
include_torsion_forces = True
constrain_bonds = False
# Bond definitions
bond_length = 1.5 * unit.angstrom
bond_lengths = {
"bb_bb_bond_length": bond_length,
"bb_sc_bond_length": bond_length,
"sc_sc_bond_length": bond_length,
}
bond_force_constant = 1000 * unit.kilojoule_per_mole / unit.nanometer / unit.nanometer
bond_force_constants = {
"bb_bb_bond_force_constant": bond_force_constant,
"bb_sc_bond_force_constant": bond_force_constant,
"sc_sc_bond_force_constant": bond_force_constant,
}
# Particle definitions
mass = 100.0 * unit.amu
r_min = 1.5 * bond_length # Lennard-Jones potential r_min
# Factor of /(2.0**(1/6)) is applied to convert r_min to sigma
sigma = r_min / (2.0**(1.0 / 6.0))
epsilon = 0.5 * unit.kilojoule_per_mole
bb = {
"particle_type_name": "bb",
"sigma": sigma,
"epsilon": epsilon,
"mass": mass
}
sc = {
"particle_type_name": "sc",
"sigma": sigma,
"epsilon": epsilon,
"mass": mass
}
# Bond angle definitions
bond_angle_force_constant = 100 * unit.kilojoule_per_mole / unit.radian / unit.radian
bond_angle_force_constants = {
"bb_bb_bb_bond_angle_force_constant": bond_angle_force_constant,
"bb_bb_sc_bond_angle_force_constant": bond_angle_force_constant,
}
# OpenMM requires angle definitions in units of radians
bb_bb_bb_equil_bond_angle = 120.0 * unit.degrees
bb_bb_sc_equil_bond_angle = 120.0 * unit.degrees
equil_bond_angles = {
"bb_bb_bb_equil_bond_angle": bb_bb_bb_equil_bond_angle,
"bb_bb_sc_equil_bond_angle": bb_bb_sc_equil_bond_angle,
}
# Torsion angle definitions
torsion_force_constant = 20.0 * unit.kilojoule_per_mole
torsion_force_constants = {
"bb_bb_bb_bb_torsion_force_constant": torsion_force_constant,
"bb_bb_bb_sc_torsion_force_constant": torsion_force_constant
}
bb_bb_bb_bb_torsion_phase_angle = 75.0 * unit.degrees
bb_bb_bb_sc_torsion_phase_angle = 75.0 * unit.degrees
torsion_phase_angles = {
"bb_bb_bb_bb_torsion_phase_angle": bb_bb_bb_bb_torsion_phase_angle,
"bb_bb_bb_sc_torsion_phase_angle": bb_bb_bb_sc_torsion_phase_angle
}
torsion_periodicities = {
"bb_bb_bb_bb_torsion_periodicity": 3,
"bb_bb_bb_sc_torsion_periodicity": 3
}
# Monomer definitions
A = {
"monomer_name": "A",
"particle_sequence": [bb, sc],
"bond_list": [[0, 1]],
"start": 0,
"end": 0,
}
sequence = 24 * [A]
pdb_path = os.path.join(data_path, "24mer_1b1s_initial_structure.pdb")
positions = PDBFile(pdb_path).getPositions()
# Build a coarse grained model
cgmodel = CGModel(
particle_type_list=[bb, sc],
bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
bond_angle_force_constants=bond_angle_force_constants,
torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
torsion_phase_angles=torsion_phase_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,
sequence=sequence,
monomer_types=[A],
)
return cgmodel
C = { # a 1-2 bead
"monomer_name": "C",
"particle_sequence": [b,c,c],
"bond_list": [[0,1], [1,2]],
"start": 0,
"end": 0,
}
sequence = 5 * [A, B, C]
# Build a coarse grained model
cgmodel = CGModel(
particle_type_list=particle_type_list,
bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
bond_angle_force_constants=bond_angle_force_constants,
torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
torsion_phase_angles=torsion_phase_angles,
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,
random_positions=random_positions,
sequence=sequence,
monomer_types=[A, B, C],
)
file_name = "20mer_ABC5_initial_structure.pdb"
write_pdbfile_without_topology(cgmodel, file_name)