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IMP Reference Guide  2.5.0
The Integrative Modeling Platform
IMP.pmi.macros.ReplicaExchange0 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 20 of file

Public Member Functions

def __init__
 Constructor. More...

Constructor & Destructor Documentation

def IMP.pmi.macros.ReplicaExchange0.__init__ (   self,
  representation = None,
  root_hier = None,
  sample_objects = None,
  monte_carlo_sample_objects = None,
  molecular_dynamics_sample_objects = None,
  output_objects = None,
  crosslink_restraints = 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,
  num_sample_rounds = 1,
  number_of_best_scoring_models = 500,
  monte_carlo_steps = 10,
  molecular_dynamics_steps = 10,
  molecular_dynamics_max_time_step = 1.0,
  number_of_frames = 1000,
  nframes_write_coordinates = 1,
  write_initial_rmf = True,
  initial_rmf_name_suffix = 'initial',
  stat_file_name_suffix = 'stat',
  best_pdb_name_suffix = 'model',
  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 


modelThe IMP model
representationPMI.representation.Representation object (or list of them, for multi-state modeling)
root_hierInstead of passing Representation, just pass a hierarchy
monte_carlo_sample_objectsObjects for MC sampling; a list of structural components (generally the representation) that will be moved and restraints with parameters that need to be sampled. OR a DegreesOfFreedom object!
molecular_dynamics_sample_objectsObjects for MD sampling
output_objectsA list of structural objects and restraints that will be included in output (statistics files). Any object that provides a get_output() method can be used here.
crosslink_restraintsList of cross-link restraints that will be included in output RMF files (for visualization).
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
num_sample_roundsNumber of rounds of MC/MD per cycle
number_of_best_scoring_modelsNumber of top-scoring PDB models to keep around for analysis
monte_carlo_stepsNumber of MC steps per round
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
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.

Definition at line 62 of file

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