trj_unwrap.py Command Help

Command: $SCHRODINGER/run trj_unwrap.py

usage: trj_unwrap.py [-h] [-s START:END:STEP] [-glue] [-temporal] [-asl ASL]
                     cms trj out

This script alters some atomic positions in the trajectory by performing the
requested "unwrapping" operation(s) under the system's periodic boundary
condition (PBC). Two unwrapping operations are currently supported:

* Glue
  This translates atoms so that atoms belonging to the same molecule will be
  placed at the same side of the simulation box. Besides that, solute molecules
  that were close to each other at the beginning of the simulation will be kept
  close as if there were "intermolecular" bonds. This is useful to fix molecular
  structures that were "wrapped" to the opposite sides of the box under the PBC.
  The '-glue' option activates this operation.

* Temporal
  This translates user-selected atoms so that their positions in each frame will
  be close to those in the prior frame under the PBC. This is useful to track
  atoms' displacements in the real space. The '-temporal' option activates this
  operation.

If both '-glue' and '-temporal' are specified, glue is done first.

Example:
  $SCHRODINGER/run trj_unwrap.py -glue -temporal -asl ligand test-out.cms test_trj unwrapped

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.
  -glue                 Perform the 'glue' unwrapping operation
  -temporal             Perform the 'temporal' unwrapping operation
  -asl ASL              ASL expression to specify the part of system to be
                        unwrapped by the temporal operation. Default: solute.