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The trajectories produced from a dynamics calculation generally require some sort of additional processing to make them easier to analyze. Currently, two such commands are provided, MERGE and ROTATE. MERGE is described below, and ROTATE is described under the COMPARE command, see Reorienting a Coordinate Trajectory.
Frequently, one generates a trajectory into small files to minimize the CPU time of one job. However, so many files are usually hard to manage so it is desirable to merge said files into larger units. This command provides that capacity. In addition, it is possible to break up the trajectory into smaller pieces and to sample the trajectory less frequently than originally generated.
MERGE DYN [ COOR ] [FIRSTU unit-number] [NUNIT integer] [SKIP integer]
[ VEL ] [OUTPUTU unit-number] [NFILE integer]
Option Default Purpose
[COOR] COOR Specification of the type of trajectory file. COOR is
[VEL ] coordinates; VEL is velocities.
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 times the number of
input files. WARNING: This default will generate a bad
trajectory file if SKIP is not set to the interval
actually present in the trajectories. Further, if you
set its value to be larger than the number of
coordinates that are actually written in any output
file, you will have problems. The error that is
generated results from the control array in the
beginning specifying that there are more coordinates
than actually exist in the file. EOF errors will result
when the trajectory is read.
The title of the output trajectory will be copied from the input trajectory.