plane_shear_md_driver.py Command Help

Command: $SCHRODINGER/run plane_shear_md_gui_dir/plane_shear_md_driver.py

usage: $SCHRODINGER/run plane_shear_md_gui_dir/plane_shear_md_driver.py
       [-h] -cms_file CMS_FILE -asl ASL ASL [-normal_pressure NORMAL_PRESSURE]
       [-shear_velocity SHEAR_VELOCITY] [-meta_interval META_INTERVAL]
       [-md_timestep MD_TIMESTEP] [-md_umbrella] [-md_time MD_TIME]
       [-md_trj_int MD_TRJ_INT] [-md_temp MD_TEMP] [-seed SEED]
       [-no_cms_ff_update] [-HOST <hostname>] [-D] [-VIEWNAME <viewname>]
       [-JOBNAME JOBNAME]

Set up a simulation for MD that shears two slabs using metadynamics method.
Copyright Schrodinger, LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -cms_file CMS_FILE    Input cms file (default: None)
  -asl ASL ASL          Two ASLs for atoms constituting the two slabs to be
                        sheared (default: None)
  -normal_pressure NORMAL_PRESSURE
                        Apply pressure normal to shearing plane XY (bar)
                        (default: 1.2)
  -shear_velocity SHEAR_VELOCITY
                        Target surface velocity (Ang/ps); 1 Ang/ps = 100 m/s
                        (default: 0.0125)
  -meta_interval META_INTERVAL
                        Metadynamics (csveq) output recording interval (in
                        ps). (default: 1.2)
  -md_timestep MD_TIMESTEP
                        MD timestep or near, far and outer timesteps separated
                        by comma, e.g. 1,1,3 (in picoseconds). (default: 2)

Simulation options:
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -md_time MD_TIME      MD time (in ns) of the simulation. (default: 100.0)
  -md_trj_int MD_TRJ_INT
                        MD trajectory recording interval (in ps). (default:
                        10.0)
  -md_temp MD_TEMP      Temperature (in K) of the simulations. (default:
                        300.0)
  -seed SEED            Seed for random number generator. (default: 1234)
  -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)
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
                        (default: False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)