morphology_driver.py Command Help

Command: $SCHRODINGER/run morphology_gui_dir/morphology_driver.py

usage: $SCHRODINGER/run morphology_gui_dir/morphology_driver.py
       [-h] [-miller_planes MILLER_PLANES]
       [-miller_planes_loaded MILLER_PLANES_LOADED] [-loaded_file PATH]
       [-cell_extent CELL EXTENT] [-slab_thickness C-AXIS LENGTH UNITS]
       [-vacuum_thickness C-AXIS LENGTH UNITS] [-md_temp MD_TEMP]
       [-md_time MD_TIME] [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT]
       [-seed SEED] [-save_trj_data {none,cms,trj}] [-forcefield FORCE_FIELD]
       [-split_components] [-md_umbrella] [-energy_avg PERCENT]
       [-OPLSDIR OPLSDIR]
       input_file

Driver to predict crystal morphology using MD Copyright Schrodinger, LLC. All
rights reserved.

positional arguments:
  input_file            Input file.

options:
  -h, -help             Show this help message and exit.
  -miller_planes MILLER_PLANES
                        List of miller planes in the JSON format. Example:
                        [[1, 0, 1], [-1, 0, 2]] (default: None)
  -miller_planes_loaded MILLER_PLANES_LOADED
                        List of miller planes in the JSON format. Example:
                        [[1, 0, 1], [-1, 0, 2]] (default: None)
  -loaded_file PATH     File containing structure(s) for the loaded Miller
                        planes (default: None)
  -cell_extent CELL EXTENT
                        Super cell extents (default: 2)
  -slab_thickness C-AXIS LENGTH UNITS
                        Specify the thickness of the slab used for this
                        surface model. This option takes a distance along the
                        plane normal in fractional coordinates. See also the
                        -bottom option. (default: 1.0)
  -vacuum_thickness C-AXIS LENGTH UNITS
                        Specify the thickness of the vacuum layer used for
                        this surface model. This option takes a distance along
                        the plane normal in fractional coordinates. (default:
                        1.0)
  -md_temp MD_TEMP      Temperature (in K) of the simulations. (default: 10.0)
  -md_time MD_TIME      MD time (in ns) of the simulation. (default: 100.0)
  -md_timestep MD_TIMESTEP
                        MD time step (in fs) of the simulations. (default:
                        1.0)
  -md_trj_int MD_TRJ_INT
                        MD trajectory recording interval (in ps). (default:
                        10.0)
  -seed SEED            Seed for random number generator. (default: 1234)
  -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)
  -forcefield FORCE_FIELD
                        Force field to use. Valid force fields are OPLS_2005,
                        S-OPLS and SPFF (default: OPLS_2005)
  -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)
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -energy_avg PERCENT   Percent from the the total trajectory to use when
                        computing interaction energy. (default: 20)

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