membrane_analysis_driver.py Command Help

Command: $SCHRODINGER/run membrane_analysis_gui_dir/membrane_analysis_driver.py

usage: $SCHRODINGER/run membrane_analysis_gui_dir/membrane_analysis_driver.py
       [-h] -cms_file CMS_FILE -trj TRJ [-trj_min TRJ_MIN] [-trj_max TRJ_MAX]
       [-trj_step TRJ_STEP] -asl ASL [-axis AXIS] [-max_dist Angstroms]
       [-min_cosine MIN_COSINE] [-apl_thickness] [-order_param ORDER_PARAM]
       [-hydrophobic_asl HYDROPHOBIC_ASL] [-HOST <hostname>] [-D]
       [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]

Script for analyzing surfactant/lipid membranes 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:
                        None)
  -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)
  -asl ASL              ASL for head group atoms. Molecules with matches are
                        considered lipids/surfactants and the matched atoms
                        are considered head groups. Bilayer thickness is
                        defined as the difference between average height of
                        head groups in each leaflet. (default: None)
  -axis AXIS            The index of axis normal to the membrane. 0 for X, 1
                        for Y and 2 for Z. If not provided, head to tail
                        orientation of surfactants will be used to find the
                        normal if you're using the min cosine and max distance
                        leaflet-finding algorithm; otherwise, when
                        -hydrophobic_asl is provided, the default axis will be
                        2. (default: None)
  -max_dist Angstroms   The maximum distance between two head groups for them
                        to be considered neighbors. Used in leaflet
                        identification. (default: 15)
  -min_cosine MIN_COSINE
                        The minimum cosine value of the angle between two
                        surfactants for them to be considered in the same
                        direction. Higher values means stricter neighboring
                        requirements. (default: 0.5)
  -apl_thickness        Calculate membrane thickness and and area per lipid.
                        (default: False)
  -order_param ORDER_PARAM
                        The input .st2 file to calculate lipids order
                        parameter (default: None)
  -hydrophobic_asl HYDROPHOBIC_ASL
                        Define the ASL for tail group atoms.Using this flag
                        finds the leaflets from the midplane, where the
                        midplane is the average z-position of tail atoms in
                        the case of a bilayer. Not using this flag defaults
                        the leaflet finding algorithm to using lipid proximity
                        and orientations; likewise, using this flag will
                        override the use of -min_cosine and -max_dist.
                        (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)