torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
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,
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,
cgmodel.system,
cgmodel.positions,
temperature_list=temperature_list,
simulation_time_step=simulation_time_step,
total_simulation_time=total_simulation_time,
exchange_frequency=exchange_frequency,
output_data=output_data,
)
else:
print("Replica output files exist")
def signac_run_replica_exchange(job):
# Run replica exchange simulation for current job parameters
# Job settings
output_directory = os.path.join(job.workspace(), "output")
if not os.path.exists(output_directory):
os.mkdir(output_directory)
overwrite_files = True # overwrite files.
# Replica exchange simulation settings
total_simulation_time = 0.05 * unit.nanosecond
simulation_time_step = 10.0 * unit.femtosecond
total_steps = int(np.floor(total_simulation_time / simulation_time_step))
output_data = os.path.join(output_directory, "output.nc")
number_replicas = 36
min_temp = 100.0 * unit.kelvin
max_temp = 500.0 * unit.kelvin
temperature_list = get_temperature_list(min_temp, max_temp,
number_replicas)
exchange_frequency = 100 # Number of steps between exchange attempts
collision_frequency = 5 / unit.picosecond
include_bond_forces = True
include_bond_angle_forces = True
include_nonbonded_forces = True
include_torsion_forces = True
constrain_bonds = False
mass = 100.0 * unit.amu
# mass and charge are defaults.
bb = {
"particle_type_name": "bb",
"sigma": job.sp.sigma_bb * unit.nanometer,
"epsilon": job.sp.epsilon_bb * unit.kilojoules_per_mole,
"mass": mass
}
sc = {
"particle_type_name": "sc",
"sigma": job.sp.sigma_sc * unit.nanometer,
"epsilon": job.sp.epsilon_sc * unit.kilojoules_per_mole,
"mass": mass
}
# Monomer definition
A = {
"monomer_name": "A",
"particle_sequence": [bb, sc],
"bond_list": [[0, 1]],
"start": 0,
"end": 0,
}
sequence = 24 * [A]
# Bond definitions
bond_lengths = {
"default_bond_length": job.sp.equil_bond_length * unit.nanometer
}
bond_force_constants = {
"default_bond_force_constant":
job.sp.k_bond * unit.kilojoule_per_mole / unit.nanometer /
unit.nanometer
}
# Bond angle definitions
bond_angle_force_constants = {
"default_bond_angle_force_constant":
job.sp.k_angle * unit.kilojoule_per_mole / unit.radian / unit.radian
}
equil_bond_angles = {
"default_equil_bond_angle": job.sp.equil_bond_angle * unit.degrees
}
# torsion angle definitions
torsion_force_constants = {
"default_torsion_force_constant":
0.0 * unit.kilojoule_per_mole,
"bb_bb_bb_bb_torsion_force_constant":
job.sp.k_torsion * unit.kilojoule_per_mole
}
torsion_phase_angles = {
"sc_bb_bb_sc_torsion_phase_angle": 0 * unit.degrees,
"bb_bb_bb_bb_torsion_phase_angle":
job.sp.torsion_phase_angle * unit.degrees,
"bb_bb_bb_sc_torsion_phase_angle": 0 * unit.degrees,
}
torsion_periodicities = {
"sc_bb_bb_sc_torsion_periodicity": job.sp.torsion_periodicity,
"bb_bb_bb_bb_torsion_periodicity": job.sp.torsion_periodicity,
"bb_bb_bb_sc_torsion_periodicity": job.sp.torsion_periodicity,
}
# Get initial positions from local file
pdb_path = os.path.join(proj_directory, "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,
sequence=sequence,
positions=positions,
monomer_types=[A],
)
# store the cg model so that we can do various analyses.
cgmodel.export(job.fn("stored_cgmodel.pkl"))
if not os.path.exists(output_data) or overwrite_files == True:
run_replica_exchange(
cgmodel.topology,
cgmodel.system,
cgmodel.positions,
friction=collision_frequency,
temperature_list=temperature_list,
simulation_time_step=simulation_time_step,
total_simulation_time=total_simulation_time,
exchange_frequency=exchange_frequency,
output_data=output_data,
)
else:
print("Replica output files exist")
def signac_run_CEI_replica_exchange(job):
# Run replica exchange simulation for current job parameters
print(f'job_parameters:')
print(job.sp)
rep_exch_begin = time.perf_counter()
# Job settings
output_directory = os.path.join(job.workspace(),"output_CEI")
if not os.path.exists(output_directory):
os.mkdir(output_directory)
overwrite_files = True # overwrite files.
global_context_cache.platform = openmm.Platform.getPlatformByName("CUDA")
# Replica exchange simulation settings
total_simulation_time = 200.0 * unit.nanosecond
simulation_time_step = 5.0 * unit.femtosecond
total_steps = int(np.floor(total_simulation_time / simulation_time_step))
output_data = os.path.join(output_directory, "output.nc")
number_replicas = job.sp.n_replica
min_temp = 200.0 * unit.kelvin
max_temp = 600.0 * unit.kelvin
# Load in CEI temperature list:
temperature_list = pickle.load(open(job.fn("opt_T_spacing.pkl"),"rb"))
exchange_frequency = job.sp.exch_freq # Number of steps between exchange attempts
collision_frequency = job.sp.coll_freq/unit.picosecond
include_bond_forces = True
include_bond_angle_forces = True
include_nonbonded_forces = True
include_torsion_forces = True
constrain_bonds = False
mass = 100.0 * unit.amu
# mass and charge are defaults.
bb = {
"particle_type_name": "bb",
"sigma": job.sp.sigma_bb * unit.angstrom,
"epsilon": job.sp.epsilon_bb * unit.kilojoules_per_mole,
"mass": mass
}
sc = {
"particle_type_name": "sc",
"sigma": job.sp.sigma_sc * unit.angstrom,
"epsilon": job.sp.epsilon_sc * unit.kilojoules_per_mole,
"mass": mass
}
# Monomer definition
A = {
"monomer_name": "A",
"particle_sequence": [bb, sc],
"bond_list": [[0, 1]],
"start": 0,
"end": 0,
}
sequence = 24 * [A]
# Bond definitions
bond_lengths = {"default_bond_length": job.sp.equil_bond_length * unit.nanometer}
bond_force_constants = {
"default_bond_force_constant": job.sp.k_bond * unit.kilojoule_per_mole / unit.nanometer / unit.nanometer
}
# Bond angle definitions
bond_angle_force_constants = {
"default_bond_angle_force_constant": job.sp.k_angle * unit.kilojoule_per_mole / unit.radian / unit.radian
}
equil_bond_angles = {
"default_equil_bond_angle": job.sp.equil_bond_angle_bb_bb_sc * unit.degrees,
"bb_bb_bb_equil_bond_angle": job.sp.equil_bond_angle_bb_bb_bb * unit.degrees}
# torsion angle definitions
torsion_force_constants = {
"default_torsion_force_constant": 0.0 * unit.kilojoule_per_mole,
"bb_bb_bb_bb_torsion_force_constant": job.sp.k_torsion * unit.kilojoule_per_mole}
# Need to substract 180 degrees from specified torsion for mdtraj consistency
torsion_phase_angles = {
"sc_bb_bb_sc_torsion_phase_angle": 0 * unit.degrees,
"bb_bb_bb_bb_torsion_phase_angle": (job.sp.equil_torsion_angle_bb_bb_bb_bb-180) * unit.degrees,
"bb_bb_bb_sc_torsion_phase_angle": 0 * unit.degrees,
}
torsion_periodicities = {
"sc_bb_bb_sc_torsion_periodicity": job.sp.torsion_periodicity,
"bb_bb_bb_bb_torsion_periodicity": job.sp.torsion_periodicity,
"bb_bb_bb_sc_torsion_periodicity": job.sp.torsion_periodicity,
}
# Get initial positions from local file
pdb_path = os.path.join(proj_directory, f"initial_structure_trial_{job.sp.trial}.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],
)
# store the cg model so that we can do various analyses.
cgmodel.export(job.fn("stored_cgmodel.pkl"))
if not os.path.exists(output_data) or overwrite_files == True:
run_replica_exchange(
cgmodel.topology,
cgmodel.system,
cgmodel.positions,
friction=collision_frequency,
temperature_list=temperature_list,
simulation_time_step=simulation_time_step,
total_simulation_time=total_simulation_time,
exchange_frequency=exchange_frequency,
output_data=output_data,
)
else:
print("Replica output files exist")
rep_exch_end = time.perf_counter()
print(f'replica exchange run time: {rep_exch_end-rep_exch_begin}')