Trajectory Processing “Run”
Like ptraj, a trajectory processing “Run” is one of the main ways to run cpptraj. First the Run is set up via commands read in from an input file or the interactive prompt. Trajectories are then read in one frame at a time (or in the case of ensemble processing all frames from a given step are read). Actions are performed on the coordinates
stored in the frame, after which any output coordinates are written. At the end of the run, any data sets generated are written, and any queued Analyses are performed.
Actions and multiple topologies
Since cpptraj supports multiple topology files, during a Run actions are set up every time the topology changes in order to recalculate things like what atoms are in a mask etc. Actions that are not valid for the current topology are skipped for that topology. So for example given two topology files with 100 residues, if the first topology file processed includes a ligand named MOL and the second one does not, the action:
distance :80 :MOL out D_80-to-MOL.dat
will be valid for the first topology but not for the second, so it will be skipped as long as the second topology is active.