electroporation_driver.py Command Help

Command: $SCHRODINGER/run electroporation_gui_dir/electroporation_driver.py

usage: $SCHRODINGER/run electroporation_gui_dir/electroporation_driver.py
       [-h] [-single_failure] [-neighbor_dist NEIGHBOR_DIST] [-field FIELD]
       [-asl ASL] [-md_temp MD_TEMP] [-md_press MD_PRESS] [-md_time MD_TIME]
       [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT] [-md_umbrella]
       [-seed SEED] [-save_trj_data {none,cms,trj}] [-no_cms_ff_update]
       [-HOST <hostname>] [-D] [-JOBNAME JOBNAME]
       cms_files [cms_files ...]

Script to perform electroporation analysis Copyright Schrodinger, LLC. All
rights reserved.

positional arguments:
  cms_files             Input cms files.

options:
  -h, -help             Show this help message and exit.
  -single_failure       When multiple membranes are present, report the time
                        that the first membrane fails, as opposed to when all
                        membranes fail. (default: False)
  -neighbor_dist NEIGHBOR_DIST
                        Neighbor distance for clustering. Larger values mean
                        less strict criteria for pore formation. (default: 4)
  -field FIELD          Field strength in the Z+ direction during the
                        simulation, can be negative. (default: 0.9)
  -asl ASL              ASL for the membranes. (default: mol.atom > 20)
  -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_time MD_TIME      MD time (in ns) of the simulation. (default: 30000.0)
  -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:
                        25)
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -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:
                        trj)
  -no_cms_ff_update     Do not update the force field of an input CMS file to
                        the current version. (default: False)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)