Input to CPPTRAJ is in the form of commands, which can be categorized in to 2 types: immediate and queued. Immediate commands are executed as soon as they are encountered. Queued commands are initialized when they are encountered, but are not executed until a Run is executed via a run or go command. Actions, Analyses, and Trajectory commands (except reference) are queued commands; however, they can also be run immediately via commands such as crdaction, runanalysis, loadcrd, etc. See 28.5 on page 564 for more details.

Commands fall into seven categories:

  • General (Immediate) These commands are executed immediately when entered.
  • System (Immediate) These are unix system commands (e.g. ’ls’, ’pwd’, etc).
  • Coords (Immediate) These commands are used to manipulate COORDS data sets.
  • Trajectory (Queued) These commands prepare cpptraj for reading or writing trajectories during a Run.
  • Topology (Immediate) These commands are used to read, write, and modify topology information.
  • Action (Queued) These commands specify actions that will be performed on coordinate frames read in from trajectories during a Run.
  • Analysis (Queued) These commands specify analyses that will be performed on data that has been either generated from a Run or read in from an external source.
  • Control (Immediate) These commands set up control blocks that can be used to e.g. loop over a set of commands.

In addition to normal commands, CPPTRAJ now has the ability to perform certain basic math operations, even on data sets.

Commands in CPPTRAJ can be read in from an input file or from the interactive command prompt. A ’#’ anywhere on a line denotes a comment; anything after ’#’ will be ignored no matter where it occurs. A ’\’ allows the continuation of one line to another. For example, the input:

# Sample input
trajin mdcrd # This is a trajectory
rms first out rmsd.dat \
Translates to:
trajin mdcrd
rms first out rmsd.dat :1-10

If in interactive mode, ’help <command>’ can be used to get the associated keywords as well as an abbreviated description of the command. Most commands have a corresponding test which also serves as an example