### 18.4 Reorienting a Coordinate Trajectory

If one is interested in reorienting every set of coordinates
found in a dynamics trajectory with respect to some reference structure,
one can use the `DYNAMICS` option in conjunction with the
`COORMATCH` options in the `COMPARE` command. Whatever options
specified in the `COORMATCH` command are used to translate and/or
rotate all the coordinates in the trajectory. The matching of the two
PSF's determines which atom pairs are used in the fit.

The process of reorienting a coordinate trajectory works as
follows: A series of files containing the trajectory are assigned to
successive units prior to a CONGEN run. The coordinates stored therein
are presumed to have been written every `NSAVC` steps. CONGEN will
read each coordinate, select some periodically, reorient them, and write
them to successive units where each output file will have a user
specified number of coordinates. The following table lists the options
involved:

Option Default Purpose
FIRSTU 51 The first unit of the trajectory to be read.
NUNIT 1 The number of units to be read starting with FIRSTU.
SKIP 1 Only those coordinate whose dynamics step number
modulo SKIP will be reoriented and written out.
OUTPUTU 61 The first unit number of the output trajectory.
NFILE The number of coordinates written to each output file.
If left out, this will be set to the number of
coordinates in the first input file.

The title of the output trajectory will be copied from the input
trajectory.

If atoms were fixed during the dynamics, see Fixed Atoms,
the new trajectory produced will not have fixed atoms because the
rotations applied to each coordinate set will be different thereby
yielding different coordinates for the fixed atoms. Fixing the
coordinates leads to a large space reductions, so the reorientation
process will therefore result in potentially much larger trajectory
files.

When the process is complete, the comparison coordinates will be
the last set of coordinates written to the output trajectory files. This
is true even if ``COOR ``unit`' is specified. Also, if the
`SAVE` option is used, then the saved transformation will be the one
used for the last set of coordinates.