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.