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IMP Reference Guide  develop.031dafb4d2,2024/05/21
The Integrative Modeling Platform
IMP.pmi.macros.ReplicaExchange Class Reference

A macro to help setup and run replica exchange. More...

Inherits object.

Detailed Description

A macro to help setup and run replica exchange.

Supports Monte Carlo and molecular dynamics. Produces trajectory RMF files, best PDB structures, and output stat files.

This class is only available in Python.

Definition at line 70 of file

Public Member Functions

def __init__
 Constructor. More...

Constructor & Destructor Documentation

def IMP.pmi.macros.ReplicaExchange.__init__ (   self,
  monte_carlo_sample_objects = None,
  molecular_dynamics_sample_objects = None,
  output_objects = [],
  rmf_output_objects = None,
  monte_carlo_temperature = 1.0,
  simulated_annealing = False,
  simulated_annealing_minimum_temperature = 1.0,
  simulated_annealing_maximum_temperature = 2.5,
  simulated_annealing_minimum_temperature_nframes = 100,
  simulated_annealing_maximum_temperature_nframes = 100,
  replica_exchange_minimum_temperature = 1.0,
  replica_exchange_maximum_temperature = 2.5,
  replica_exchange_swap = True,
  num_sample_rounds = 1,
  number_of_best_scoring_models = 500,
  monte_carlo_steps = 10,
  self_adaptive = False,
  molecular_dynamics_steps = 10,
  molecular_dynamics_max_time_step = 1.0,
  number_of_frames = 1000,
  save_coordinates_mode = 'lowest_temperature',
  nframes_write_coordinates = 1,
  write_initial_rmf = True,
  initial_rmf_name_suffix = 'initial',
  stat_file_name_suffix = 'stat',
  best_pdb_name_suffix = 'model',
  mmcif = False,
  do_clean_first = True,
  do_create_directories = True,
  global_output_directory = './',
  rmf_dir = 'rmfs/',
  best_pdb_dir = 'pdbs/',
  replica_stat_file_suffix = 'stat_replica',
  em_object_for_rmf = None,
  atomistic = False,
  replica_exchange_object = None,
  test_mode = False,
  score_moved = False,
  use_nestor = False,
  nestor_restraints = None,
  nestor_rmf_fname_prefix = 'nested' 


modelThe IMP model
root_hierTop-level (System)hierarchy
monte_carlo_sample_objectsObjects for MC sampling, which should generally be a simple list of Mover objects, e.g. from DegreesOfFreedom.get_movers().
molecular_dynamics_sample_objectsObjects for MD sampling, which should generally be a simple list of particles.
output_objectsA list of structural objects and restraints that will be included in output (ie, statistics "stat" files). Any object that provides a get_output() method can be used here. If None is passed the macro will not write stat files.
rmf_output_objectsA list of structural objects and restraints that will be included in rmf. Any object that provides a get_output() method can be used here.
monte_carlo_temperatureMC temp (may need to be optimized based on post-sampling analysis)
simulated_annealingIf True, perform simulated annealing
simulated_annealing_minimum_temperatureShould generally be the same as monte_carlo_temperature.
simulated_annealing_minimum_temperature_nframesNumber of frames to compute at minimum temperature.
simulated_annealing_maximum_temperature_nframesNumber of frames to compute at temps > simulated_annealing_maximum_temperature.
replica_exchange_minimum_temperatureLow temp for REX; should generally be the same as monte_carlo_temperature.
replica_exchange_maximum_temperatureHigh temp for REX
replica_exchange_swapBoolean, enable disable temperature swap (Default=True)
num_sample_roundsNumber of rounds of MC/MD per cycle
number_of_best_scoring_modelsNumber of top-scoring PDB/mmCIF models to keep around for analysis.
mmcifIf True, write best scoring models in mmCIF format; if False (the default), write in legacy PDB format.
best_pdb_dirThe directory under global_output_directory where best-scoring PDB/mmCIF files are written.
best_pdb_name_suffixPart of the file name for best-scoring PDB/mmCIF files.
monte_carlo_stepsNumber of MC steps per round
self_adaptiveself adaptive scheme for Monte Carlo movers
molecular_dynamics_stepsNumber of MD steps per round
molecular_dynamics_max_time_stepMax time step for MD
number_of_framesNumber of REX frames to run
save_coordinates_modestring: how to save coordinates. "lowest_temperature" (default) only the lowest temperatures is saved "25th_score" all replicas whose score is below the 25th percentile "50th_score" all replicas whose score is below the 50th percentile "75th_score" all replicas whose score is below the 75th percentile
nframes_write_coordinatesHow often to write the coordinates of a frame
write_initial_rmfWrite the initial configuration
global_output_directoryFolder that will be created to house output.
test_modeSet to True to avoid writing any files, just test one frame.
score_movedIf True, attempt to speed up Monte Carlo sampling by caching scoring function terms on particles that didn't move.
use_nestorIf True, follows the Nested Sampling workflow of the NestOR module and skips writing stat files and replica stat files.
nestor_restraintsA list of restraints for which likelihoods are to be computed for use by NestOR module.
nestor_rmf_fname_prefixPrefix to be used for storing .rmf3 files generated by NestOR .

Definition at line 142 of file

The documentation for this class was generated from the following file: