analyze_simulation.py Command Help

Command: $SCHRODINGER/run analyze_simulation.py

usage: analyze_simulation.py [-h] [-HOST <hostname>] [-WAIT] [-LOCAL] [-D]
                             [-NOJOBID] [-VIEWNAME <viewname>]
                             [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
                             [-s START:END:STEP] [-sim-cfg SIM_CFG]
                             cms trj out st2

Perform geometric analyses and energy group analyses on simulation trajectory.

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
  st2                   Input .st2 or .eaf file name

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.
  -sim-cfg SIM_CFG      Simulation configuration file, i.e., a Desmond cfg
                        file.

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.