electrolyte_analysis_driver.py Command Help

Command: $SCHRODINGER/run electrolyte_analysis_gui_dir/electrolyte_analysis_driver.py

usage: $SCHRODINGER/run electrolyte_analysis_gui_dir/electrolyte_analysis_driver.py
       [-h] -cms_file CMS_FILE -trj TRJ [-trj_min TRJ_MIN] [-trj_max TRJ_MAX]
       [-trj_step TRJ_STEP] -ion_mol ION_MOL [-ion_atom ION_ATOM]
       -counterion_mol COUNTERION_MOL
       [-counterion_elements COUNTERION_ELEMENTS]
       [-chain_elements CHAIN_ELEMENTS] [-cutoff CUTOFF]
       [-vis_cutoff VIS_CUTOFF] [-density_isosurf] [-rdf] [-rdf_distance]
       [-resolution INT] [-rdf_resolution RDF_RESOLUTION]
       [-rdf_max_dist RDF_MAX_DIST] [-sq] [-num_waves NUM_WAVES]
       [-residence_time] [-cluster_composition] [-merge_clusters]
       [-HOST <hostname>] [-D] [-JOBNAME JOBNAME]

Script to get information about clusters surrounding ions Copyright
Schrodinger, LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -cms_file CMS_FILE    Input cms file (default: None)
  -trj TRJ              Directory of the trajectory (default: None)
  -trj_min TRJ_MIN      Minimum of trajectory frame to be analysed. (default:
                        0)
  -trj_max TRJ_MAX      Maximum of trajectory frame to be analysed. (default:
                        None)
  -trj_step TRJ_STEP    Use every n-th frame in the trajectory range. The
                        first and last frames in the range will always be
                        included. (default: None)
  -ion_mol ION_MOL      The molecule number for an ion in the structure.
                        (default: None)
  -ion_atom ION_ATOM    The ion atom for which the coordination should be
                        calculated. Required if the ion is polyatomic
                        (default: None)
  -counterion_mol COUNTERION_MOL
                        The molecule number for a counterion in the structure.
                        (default: None)
  -counterion_elements COUNTERION_ELEMENTS
                        The coordination elements for the counterion.
                        (default: ['O'])
  -chain_elements CHAIN_ELEMENTS
                        The coordination elements for chains. (default: ['O'])
  -cutoff CUTOFF        The cutoff for coordination calculations. (default:
                        3.3)
  -vis_cutoff VIS_CUTOFF
                        The cutoff for cluster visualization. (default: 3.3)
  -density_isosurf      Generate density isosurface. (default: False)
  -rdf                  Calculate the RDF between the selected atom of the
                        transference ion and all coordination elements.
                        (default: False)
  -rdf_distance         Use the distance from the maximum peak of the RDF
                        function. If not provided, the coordination cutoff
                        will be used instead. (default: False)
  -resolution INT       Resolution of the density isosurface, defined by the
                        approximate spacing between grid points used to
                        generate the isosurface. (default: 1.0)
  -rdf_resolution RDF_RESOLUTION
                        Bin width for the RDF calculation. (default: 0.1)
  -rdf_max_dist RDF_MAX_DIST
                        Maximum distance for the RDF calculation. (default:
                        20.0)
  -sq                   Calculate structure factor S(q). (default: False)
  -num_waves NUM_WAVES  Number of waves in each dimension for S(q). (default:
                        20)
  -residence_time       Calculate residence time for molecules coordinating
                        with transference ions. (default: False)
  -cluster_composition  Calculate cluster composition as molecules
                        coordinating with transference ions. (default: False)
  -merge_clusters       Merge clusters when transference ions are within each
                        other's coordination cutoff. (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)