if two actions specify the same data file with the 'out' keyword, data from both actions will be written to that data file). In addition, users can control which data sets are written to which files (e.g. Users usually are able to fine-tune the output format of data files declared in actions using the “ out” keyword (for example, the precision of the numbers can be changed).Actions that modify coordinates and topology such as the strip/ closest actions can often write an accompanying fully-functional stripped topology file.In addition, per-residue RMSD can be calculated easily. The rmsd action allows specification of a separate mask for the reference structure.Specific frames from trajectories may be used as a reference structure. Multiple reference structures can be specified.In addition, output files can be directed to write only specific frames from the input trajectories. Multiple output trajectories can be specified, and can be written during action processing (as opposed to only after) via the outtraj command.

A trajectory can be written in DCD format if the '.dcd' extension is used. For example, data files can be written in xmgrace format if the filename given has a '.agr' extension. The format of output data files can be specified by extension.Compression is detected automatically when reading, and is determined by the filename extension (.gz and. So for example gzipped/bzipped topology files can be read, and data files can be written out as gzip/bzip2 files. Almost any file read or written by cpptraj can be compressed (with the exception of the NetCDF trajectory format).Trajectory and ensemble reads can be MPI parallelized.Several actions/analyses in cpptraj are OpenMP parallelized see section 2.7.2 for more details.Trajectories with different topologies can be processed in the same run.Here are several notable features of cpptraj:

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