mc_sa_driver.py Command Help

Command: $SCHRODINGER/run mc_sa_gui_dir/mc_sa_driver.py

usage: $SCHRODINGER/run mc_sa_gui_dir/mc_sa_driver.py [-h] [-minimize]
                                                      [-forcefield FORCE_FIELD]
                                                      [-max_structs MAX_STRUCTS]
                                                      [-energy_window ENERGY_WINDOW]
                                                      [-weights ROTATION:TRANSLATION]
                                                      [-max_rotation DEGREES]
                                                      [-translation_mu MEAN]
                                                      [-translation_sigma STDDEV]
                                                      [-temperatures TEMP:TEMP:TEMP]
                                                      [-iterations ITERATIONS]
                                                      [-scale_vdw VDW_SCALE_FACTOR]
                                                      [-substrate_radius SUBSTRATE_RADIUS]
                                                      [-finite]
                                                      [-prepare_desmond]
                                                      [-seed SEED]
                                                      [-split_components]
                                                      [-HOST <hostname>]
                                                      input_file output_file

Driver for the Monte Carlo Simulated Annealing Copyright Schrodinger, LLC. All
rights reserved.

positional arguments:
  input_file            Input file.
  output_file           Output file. This file will contain structures with
                        the computed properties.

options:
  -h, -help             Show this help message and exit.
  -minimize             Minimize the resulting structures using the requested
                        force field. The default is not to minimize the
                        system. (default: False)
  -forcefield FORCE_FIELD
                        Force field to use in energy evaluations. Valid force
                        fields are OPLS_2005, S-OPLS, SPFF,
                        MLFF:official:Hybrid_MPNICE,
                        MLFF:official:Hybrid_MPNICE_I,
                        MLFF:official:Hybrid_MPNICE_O,
                        MLFF:official:Inorganic_MPNICE,
                        MLFF:official:Organic_Crystals_MPNICE and
                        MLFF:official:Organic_MPNICE (default: OPLS_2005)
  -max_structs MAX_STRUCTS
                        Number of low-energy structures to be saved. (default:
                        10)
  -energy_window ENERGY_WINDOW
                        Number of low-energy structures to be saved. (default:
                        None)
  -weights ROTATION:TRANSLATION
                        A colon-delimited list of 2 numbers that defines the
                        relative frequency of rotations and translations
                        during Monte Carlo annealing, with the first value
                        being the weight for rotations.Rotation rotates a
                        molecule randomly, keeping the center of the molecule
                        fixed. Translation moves the molecule randomly,
                        keeping the rotation fixed. A value of 0 for any
                        weight means that type of move will not be performed.
                        The default value of 0.5:0.5 indicates that rotation
                        and translation are equally likely. (default: 0.5:0.5)
  -max_rotation DEGREES
                        The maximum rotation in degrees allowed when
                        performing a rotation step in the Monte Carlo
                        annealing. The default is 360.0. (default: 360.0)
  -translation_mu MEAN  The value of mu in the log-normal distribution that
                        determines the translation step size. mu gives the
                        mean value of the distribution. The default mu and
                        sigma values of 0.25 and 1.00 give maximum probability
                        to values around 0.5 Angstrom, 40 percent chance of
                        translations of 1 Angstrom or less, and about a 5
                        percent chance of translations larger than 7 Angstrom.
                        (default: 0.25)
  -translation_sigma STDDEV
                        The value of sigma in the log-normal distribution that
                        determines the translation step size. sigma gives the
                        standard deviation of the distribution. The default mu
                        and sigma values of 0.25 and 1.00 give maximum
                        probability to values around 0.5 Angstrom, 40 percent
                        chance of translations of 1 Angstrom or less, and
                        about a 5 percent chance of translations larger than 7
                        Angstrom. (default: 1.0)
  -temperatures TEMP:TEMP:TEMP
                        A colon-delimited list of temperatures in K that the
                        Monte Carlo simulated annealing should be run at. The
                        number of iterations at each step is given by
                        -iterations. (default: 900:600:300)
  -iterations ITERATIONS
                        The number of Monte Carlo iterations to run during
                        Monte Carlo annealing. (default: 3000)
  -scale_vdw VDW_SCALE_FACTOR
                        Scale factor for VDW radii to use when computing
                        clashes. The default is 1.0. (default: 1.0)
  -substrate_radius SUBSTRATE_RADIUS
                        Surface radius to limit Monte Carlo sampling space
                        around substrate. (default: None)
  -finite               Treat system as finite. (default: False)
  -prepare_desmond      Prepare final structures for use in Desmond
                        simulations. (default: False)
  -seed SEED            Seed for random number generator. (default: 1234)
  -split_components     Split system in components when Desmond system is
                        built. This can speed up the the force field
                        assignment for systems that contain multiple identical
                        molecules. (default: False)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)