droplet_contact_analysis_driver.py Command Help

Command: $SCHRODINGER/run droplet_contact_analysis_gui_dir/droplet_contact_analysis_driver.py

usage: $SCHRODINGER/run droplet_contact_analysis_gui_dir/droplet_contact_analysis_driver.py
       [-h] [-trj TRJ] [-droplet DROPLET | -solvent SOLVENT]
       [-sol_density SOL_DENSITY] [-num_mols NUM_MOLS]
       [-initial_vel INITIAL_VEL] [-bin_width BIN_WIDTH] [-max_dist MAX_DIST]
       [-skip_time SKIP_TIME] [-md_temp MD_TEMP] [-md_time MD_TIME]
       [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT] [-seed SEED]
       [-md_umbrella] [-water_fftype WATER_TYPE] [-force_c FORCE_C]
       [-save_trj_data {none,cms,trj}] [-forcefield FORCE_FIELD]
       [-enable_metal_force_field] [-substrate_asl SUBSTRATE_ASL]
       [-cgffld FORCE_FIELD_NAME] [-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE]
       [-HOST <hostname>] [-D] [-JOBNAME JOBNAME]
       input_file

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

positional arguments:
  input_file            Input structure file.

options:
  -h, -help             Show this help message and exit.
  -trj TRJ              Path to existing trajectory directory when a new
                        simulation should not be performed. (default: None)
  -droplet DROPLET      Droplet structure file. Solvent is ignored if droplet
                        is provided. (default: None)
  -solvent SOLVENT      Name of a builtin solvent, or path to the solvent
                        structure when using a custom solvent. (default:
                        water)
  -sol_density SOL_DENSITY
                        Bulk density for the custom solvent. Used for droplet
                        packing. (default: 1)
  -num_mols NUM_MOLS    Number of molecules in the droplet. (default: 3000)
  -initial_vel INITIAL_VEL
                        Initial atomic velocity component (A/ps) along the
                        interface normal towards substrate. (default: 0.5)
  -bin_width BIN_WIDTH  Bin width for density descretization and equimolar
                        surface calculation. (default: 1)
  -max_dist MAX_DIST    Molecules that are further that this value from the
                        droplet are excluded from analysis. (default: 3.5)
  -skip_time SKIP_TIME  Skip this amount of time before analyzing MD results.
                        (default: 100)
  -cgffld FORCE_FIELD_NAME
                        Name of coarse-grained force field to use. See related
                        location type flag -cgffld_loc_type. (default: None)
  -cgffld_loc_type FORCE_FIELD_LOCATION_TYPE
                        Location type for the force field specified with
                        -cgffld. Option installed means from a standard
                        location in the Schrodinger installation, while option
                        local means either from /Users/aoza/.schrodinger/matsc
                        i_templates/coarse_grain_force_field_parameters or the
                        job launch directory, i.e. the CWD. (default: local)

Simulation options:
  -md_temp MD_TEMP      Temperature (in K) of the simulations. (default:
                        300.0)
  -md_time MD_TIME      MD time (in ns) of the simulation. (default: 5000.0)
  -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:
                        10.0)
  -seed SEED            Seed for random number generator. (default: 1234)
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -water_fftype WATER_TYPE
                        Force field type for water molecules. Must be used
                        with -split_components. If using "none", the Residue
                        Name atom property is used instead. (default: SPC)
  -force_c FORCE_C      Force constant (kcal mol-1 Å-2) to use for the
                        substrate positional restraints. (default: 500)
  -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)
  -forcefield FORCE_FIELD
                        Force field to use. Valid force fields are OPLS_2005,
                        S-OPLS and SPFF (default: OPLS_2005)
  -enable_metal_force_field
                        Use the metal force field for metal atoms. This is
                        only relevant if using OPLS5, and if not specified
                        then the standard OPLS5 force field will be used for
                        all atoms including metals. (default: False)
  -substrate_asl SUBSTRATE_ASL
                        ASL for the substrate to apply positional restraints.
                        (default: None)

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)