prepare_for_md_driver.py Command Help

Command: $SCHRODINGER/run prepare_for_md_gui_dir/prepare_for_md_driver.py

usage: $SCHRODINGER/run prepare_for_md_gui_dir/prepare_for_md_driver.py
       [-h] [-forcefield FORCE_FIELD_NAME]
       [-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE] [-split_components]
       [-water_fftype WATER_TYPE] [-hydrogen_mass_repartition] [-monomer_ff_q]
       [-ewald] [-adapt_ff] [-scale] [-ortho]
       [-build_geometry_msj BUILD_GEOMETRY_MSJ] [-HOST <hostname>] [-D]
       [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
       input_file

A short driver that runs multisim on an input file to create a Desmond system
Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file exclusively containing either atomistic or
                        coarse-grained structures but not both. By default
                        assumes atomistic structures.

options:
  -h, -help             Show this help message and exit.
  -forcefield FORCE_FIELD_NAME
                        Force field to use. For atomistic systems valid force
                        fields are OPLS_2005, S-OPLS, SPFF,
                        MLFF:official:Hybrid_MPNICE,
                        MLFF:official:Hybrid_MPNICE_I,
                        MLFF:official:Hybrid_MPNICE_O,
                        MLFF:official:Inorganic_MPNICE,
                        MLFF:official:Organic_Crystals_MPNICE and
                        MLFF:official:Organic_MPNICE. For coarse-grained
                        systems specify the name of a coarse-grained force
                        field (see related location type flag
                        -cgffld_loc_type.) (default: OPLS_2005)
  -cgffld_loc_type FORCE_FIELD_LOCATION_TYPE
                        Location type for a specified coarse-grained force
                        field. Option "installed" means from a standard
                        location in the Schrodinger installation while option
                        "local" means either from /Users/bozhang/.schrodinger/
                        matsci_templates/coarse_grain_force_field_parameters
                        or the job launch directory, i.e. the CWD. (default:
                        local)
  -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)
  -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)
  -hydrogen_mass_repartition
                        Redistribute hydrogen mass to heavy atoms (default:
                        False)
  -monomer_ff_q         Use forcefield charges computed for the monomer for
                        the polymer. This option is particularly useful for
                        S-OPLS, which uses OPLS_2005 charges by default for
                        molecules larger than 100 heavy atoms. (default:
                        False)
  -ewald                Particle mesh Ewald (PME) method is used to compute
                        long-range electrostatic interactions in coarse-
                        grained MARTINI. (default: False)
  -adapt_ff             Applies structure specific modifications to the FF
                        after its raw application to the given structure.
                        (default: False)
  -scale                Scale the system to the density to reflect the reduced
                        density and cutoff values in the force field.
                        (default: False)
  -ortho                Enforce an orthorhombic PBC by zeroing out off-
                        diagonal elements (default: False)
  -build_geometry_msj BUILD_GEOMETRY_MSJ
                        MSJ file containing build_geometry stage. (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)
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
                        (default: None)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)