rdf.py Command Help

Command: $SCHRODINGER/run rdf.py

usage: rdf.py [-h] [-HOST <hostname>] [-WAIT] [-LOCAL] [-D] [-NOJOBID]
              [-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
              [-s START:END:STEP] -sel1 <ASL> [-sel2 <ASL>]
              [-pos-type1 {atom,com,coc,centroid}]
              [-pos-type2 {atom,com,coc,centroid}] [-rmax <float>]
              [-dr <float>] [-group-type1 {molecule,residue}]
              [-group-type2 {molecule,residue}]
              cms trj out

Calculate the radial distribution function of selected atoms.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  cms                   Input .cms file name
  trj                   Input trajectory file or dir name, which typically
                        ends with an extension name of '.xtc' (XTC format) or
                        '_trj' (DTR format), e.g., jobname.xtc, jobname_trj
  out                   Output file basename

options:
  -h, --help            show this help message and exit
  -s START:END:STEP, -slice-trj START:END:STEP
                        Use the sliced trajectory. We use Python's slice
                        notation. START, END, and STEP should be integer
                        numbers.
  -sel1 <ASL>           (Required) Selection of atoms in group 1 will be used
                        for the calculations. If -sel2 option is not
                        specified, then the pairwise distances within this
                        selection will be used in the RDF calculation.
  -sel2 <ASL>           (Optional) Selection of atoms in group 2. The RDF of
                        this selection will be calculated with respect to
                        -sel1 selection. This atom group is ignored if both
                        the ASL result and position type are identical to the
                        first atom group. Partial overlap between the two
                        groups is not allowed.
  -pos-type1 {atom,com,coc,centroid}
                        Position type for group 1 atoms. atom = atomic
                        position; com = molecular center of mass; coc =
                        molecular center of charge (for charged species);
                        centroid = molecular centroid.
  -pos-type2 {atom,com,coc,centroid}
                        Position type for group 2 atoms. atom = atomic
                        position; com = molecular center of mass; coc =
                        molecular center of charge (for charged species);
                        centroid = molecular centroid.
  -rmax <float>         The maximum distance (in Angstroms). The RDF will be
                        evaluated from 0 to this value. Default: 12
  -dr <float>           The bin width (in Angstroms) used in the histogram.
                        Default: 0.1
  -group-type1 {molecule,residue}
                        For "-pos-type1" set to "atom", each atom is
                        considered individually, and no grouping is performed.
                        For "-pos-type1" set to "com", "coc", or "centroid",
                        atoms are grouped into molecules or residues as per
                        "-group-type1" requested. E.g., for "-pos-type1"="com"
                        and "-group-type1"="molecule", atoms are grouped by
                        their molecular identity, and the center of mass of
                        each molecule is used in calculations.
  -group-type2 {molecule,residue}
                        For "-pos-type2" set to "atom", each atom is
                        considered individually, and no grouping is performed.
                        For "-pos-type2" set to "com", "coc", or "centroid",
                        atoms are grouped into molecules or residues as per
                        "-group-type2" requested. E.g., for "-pos-type2"="com"
                        and "-group-type2"="molecule", atoms are grouped by
                        their molecular identity, and the center of mass of
                        each molecule is used in calculations.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -LOCAL                Do not use a temporary directory for job files. Keep
                        files in the current directory.
  -D, -DEBUG            Show details of Job Control operation.
  -NOJOBID              Run the job directly, without Job Control layer.
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
  -JOBNAME JOBNAME      Provide an explicit name for the job.