trj_center.py Command Help

Command: $SCHRODINGER/run trj_center.py

usage: trj_center.py [-h] [-t TRJ] [-s START:END:STEP] [-asl ASL] cms out

Translates all atoms so that the specified atoms stay in the center (origin) of
the simulation box. By default, the selected atoms are all "solute" atoms. If
it's a membrane system, the aforementioned translation will be done only at the
x and y directions, and an additional translation will be done only at the z
direction so that the membrane will be at the center along the z axis.
This script will create a new .cms file for the translated system. If the
original system has a trajectory, it will optionally do the same for all
frames and create a new trajectory with the translated frames.

positional arguments:
  cms                   Input .cms file name
  out                   Output file basename

options:
  -h, --help            show this help message and exit
  -t TRJ, -trj 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
  -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.
  -asl ASL              ASL expression to specify the part of system to be
                        centered. Default is solute.