General Commands

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.