penetrant_loading_driver.py Command Help

Command: $SCHRODINGER/run penetrant_loading_gui_dir/penetrant_loading_driver.py

usage: $SCHRODINGER/run penetrant_loading_gui_dir/penetrant_loading_driver.py
       [-h] [-md_time NANOSECONDS] [-md_temp MD_TEMP] [-md_press MD_PRESS]
       [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT]
       [-md_ensemble ENSEMBLE] [-md_isotropy ISOTROPY_POLICY]
       [-save_trj_data {none,cms,trj}] [-seed SEED] [-md_umbrella]
       [-no_cms_ff_update]
       [-vapor VAPOR_PRESSURE_kPa | -humidity RELATIVE_HUMIDITY_%]
       [-mu_excess MU_EXCESS] [-penetrant PENETRANT] [-OPLSDIR OPLSDIR]
       input_file

Load a penetrant using Grand Canonical Monte Carlo algorithm. Copyright
Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -md_time NANOSECONDS  Simulation time for MD equilibration step (default:
                        20.0)
  -md_temp MD_TEMP      Temperature (in K) of the simulations. (default:
                        300.0)
  -md_press MD_PRESS    Pressure (in bar) of the simulations. (default:
                        1.01325)
  -md_timestep MD_TIMESTEP
                        MD time step (in fs) of the simulations. (default:
                        2.0)
  -md_trj_int MD_TRJ_INT
                        MD trajectory recording interval (in ps). (default:
                        10.0)
  -md_ensemble ENSEMBLE
                        Desmond ensemble. Known values are: NVE, NVT, NPT
                        (default: NPT)
  -md_isotropy ISOTROPY_POLICY
                        Desmond barostat isotropy policy. Known values are:
                        isotropic, semi_isotropic, constant_axis_a,
                        constant_axis_b, constant_axis_c, anisotropic,
                        flexible (default: isotropic)
  -save_trj_data {none,cms,trj}
                        Specify whether intermediate CMS or trajectory files
                        be included with the job output. Choices are none
                        (save no files), cms (save .cms files) and trj (save
                        .cms and trajectory files). Default is none. (default:
                        none)
  -seed SEED            Seed for random number generator. (default: 1234)
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -no_cms_ff_update     Do not update the force field of an input CMS file to
                        the current version. (default: False)
  -vapor VAPOR_PRESSURE_kPa
                        Vapor pressure of water in kPa. If neither -vapor or
                        -humidity are given, the saturated vapor pressure at
                        the temperature given by -md_temp will be used.
                        (default: None)
  -humidity RELATIVE_HUMIDITY_%
                        Percent relative humidity. If neither -vapor or
                        -humidity are given, the saturated vapor pressure at
                        the temperature given by -md_temp will be used.
                        (default: 100.0)
  -mu_excess MU_EXCESS  Mu-excess in kcal/mol. (default: -6.201)
  -penetrant PENETRANT  Custom penetrant file. (default: None)

Job Control Options:
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
                        (default: None)