surface_tension_driver.py Command Help

Command: $SCHRODINGER/run surface_tension_gui_dir/surface_tension_driver.py

usage: $SCHRODINGER/run surface_tension_gui_dir/surface_tension_driver.py
       [-h] [-single_component] [-solvent SOLVENT]
       [-solvent_mol_num SOLVENT_MOL_NUM] [-interface_buffer INTERFACE_BUFFER]
       [-fixed_area {XY-plane,YZ-plane,XZ-plane}]
       [-normal_pressure NORMAL_PRESSURE] [-add_relaxation_step]
       [-coulomb {useries,pme}] [-coulomb_cutoff COULOMB_CUTOFF]
       [-md_time MD_TIME] [-md_temp MD_TEMP] [-md_press MD_PRESS]
       [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT]
       [-md_enegrp_int MD_ENEGRP_INT] [-seed SEED]
       [-save_trj_data {none,cms,trj}] [-combine_trj] [-md_umbrella]
       [-no_cms_ff_update] [-HOST <hostname>] [-OPLSDIR OPLSDIR]
       input_file

driver for performing surface tension calculations Copyright Schrodinger, LLC.
All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -single_component     Compute surface tension with vacuum. (default: False)
  -solvent SOLVENT      Solvent molecule structure file if solvation is
                        requested. (default: None)
  -solvent_mol_num SOLVENT_MOL_NUM
                        Total number of solvent molecules to be added to
                        create an interface. (default: None)
  -interface_buffer INTERFACE_BUFFER
                        Additional length to be added normal to constant area
                        plane to create an interface. (default: None)
  -fixed_area {XY-plane,YZ-plane,XZ-plane}
                        Direction perpendicular to the solute-solvent surface.
                        Only in the defined direction, system length will
                        change anisotropically. Area tangential to solute-
                        solvent surface will not change (default: XY-plane)
  -normal_pressure NORMAL_PRESSURE
                        Pressure normal to fixed plane in the unit of bar.
                        Length normal to fixed area is allowed to change.
                        (default: 1.013)
  -add_relaxation_step  Add relaxation schedule before starting production
                        simulation. (default: False)
  -coulomb {useries,pme}
                        Choose Coulomb method for calculation of electrostatic
                        interaction. (default: useries)
  -coulomb_cutoff COULOMB_CUTOFF
                        Cutoff radius for the calculation of real part of
                        coulomb interaction. (default: 9.0)
  -md_time MD_TIME      MD time (in ns) of the simulation. (default: 100.0)
  -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_enegrp_int MD_ENEGRP_INT
                        MD energy group 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)
  -combine_trj          Merge all trajectories into a single one. (default:
                        False)
  -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)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
                        (default: None)