The following general commands are available:
| Command | Description |
| activeref | Select the reference for distance-based masks. |
| calc | Evaluate the given mathematical expression. |
| clear | Clear various objects from the CPPTRAJ state. |
| create | Create (but do not yet write) a data file. |
| createset | Create a dataset from a simple mathematical expression. |
| datafile | Used to manipulate data files. |
| datafilter | Filter data sets based on given criteria. |
| dataset | Use to manipulate data sets. |
| debug | prnlev | Set debug level. Higher levels give more info. |
| ensextension | Enable/disable ensemble number extension for les in ensemble mode. |
| exit | quit | Quit CPPTRAJ. |
| flatten | Distribute elements of 2d matrix across 1d array. |
| go | run | Start a trajectory processing run. Begin trajectory processing, followed by analysis and datafile write. |
| help | Provide help for commands. |
| list | List various objects in the CPPTRAJ state. |
| noexitonerror | Attempt to continue even if errors are encountered. |
| noprogress | Do not print a progress bar during a run. |
| parallelanalysis | (MPI only) Divide current Analyses among MPI processes. |
| parsetiming | Parse timing data from CPPTRAJ output. |
| precision | Change the output precision of data sets. |
| random | Set the default random number generator used in CPPTRAJ. |
| printdata | Print data set to screen. |
| readdata | Read data sets from files. |
| readensembledata | Read data files in ensemble mode. |
| readinput | Read CPPTRAJ input from a file. |
| removedata | Remove specified data set(s). |
| rst | Generate Amber-style distance/angle/torsion restraints. |
| runanalysis | Run an analysis immediately or run all queued analyses. |
| select | Print the results of an atom mask expression. |
| selectds | Print the results of a data set selection expression. |
| silenceactions | Prevent Actions from writing information to STDOUT. |
| sortensembledata | Sort data sets using replica information (currently constant pH only). |
| usediskcache | Turn caching of data sets to disk on or off. |
| write | writedata | Immediately write data to a file or write to all current data files. |