trj_merge.py Command Help

Command: $SCHRODINGER/run trj_merge.py

usage: trj_merge.py [-h] [-output-trajectory-format {dtr,xtc}]
                    [-concat start_time time_interval] [-s START:END:STEP]
                    [-o OUT]
                    cms traj [traj ...]

Merge Desmond trajectories.
This script operates in two modes:

* In the default mode, the chemical time of each frame is preserved and the
  new trajectory will have the frames sorted by chemical time. If multiple frames
  have the same chemical time, the one from the right most trajectory in the
  command line input will be used.
* In the concatenation mode, all chemical times will be overwritten by the
  user input and there is no sorting on the original chemical times. Its typical
  usage is to create an ensemble where the frames' times are irrelevant.

Examples::

  $SCHRODINGER/run trj_merge.py test-out.cms run1_trj run2_trj run3_trj
  $SCHRODINGER/run trj_merge.py jobname-out.cms run1_trj run2.xtc run3_trj -o merged -concat 0 5

The resultant cms file and trajectory are saved to the paths specified by the
-o option.

If only one trajectory is given, this script can be used to

* Associate cms file and trajectory
* Slice the trajectory

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  cms                   Input .cms file name
  traj                  Paths to input trajectories, which typically end with
                        an extension name of '.xtc' (XTC format) or '_trj'
                        (DTR format), e.g., jobname_trj, jobname.xtc

options:
  -h, --help            show this help message and exit
  -output-trajectory-format {dtr,xtc}
                        Output trajectory format. Default: "dtr"
  -concat start_time time_interval
                        Switch on the concatenation mode. In this mode, the
                        script will concatenate trajectories and reset
                        chemical time (in picosecond) for each frame.
  -s START:END:STEP, -slice-trj START:END:STEP
                        Slice the resultant trajectory. We use Python's slice
                        notation. START, END, and STEP should be integer
                        numbers.
  -o OUT                Output base name. Default: out. An appropriate
                        extension name will be added to the base name.