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Report chirality around alpha carbons in amino acids (L, D). Set or overwrite box information for frames.Ĭenter specified coordinates to box center or onto reference structure.Ĭheck for bad atomic overlaps or bond lengths. Print Urey-Bradley info for selected atoms.Ĭhange which molecules are considered solvent.Ĭalculate the angle between three points.Ĭalculate area per molecule for molecules in a specified plane.Ĭalculate average correlation between motions of specified atoms.Ĭalculate root mean square fluctuation of specified atoms/residues.Īttempt to create a map between atoms in molecules with different atom ordering.Ĭalculate the min/max coordinates for specified atoms. \begin_inset Separator latexpar\end_insetĬompare two topologies and report differences.

Note that a similar command that can be used with data generated by Actions during trajectory processing is filter (see page 1↓). Immediately write data to a file or write to all current data files. Turn caching of data sets to disk on or off. Sort data sets using replica information (currently constant pH only). Prevent Actions from writing information to STDOUT. Print the results of a data set selection expression. Print the results of an atom mask expression. Run an analysis immediately or run all queued analyses. Generate Amber-style distance/angle/torsion restraints. (MPI only) Divide current Analyses among MPI processes.Ĭhange the output precision of data sets. List various objects in the cpptraj state.Īttempt to continue even if errors are encountered.ĭo not print a progress bar during a Run. Higher levels give more info.Įnable/disable ensemble number extension for files in ensemble mode. Select the reference for distance-based masks.Įvaluate the given mathematical expression.Ĭlear various objects from the cpptraj state.Ĭreate (but do not yet write) a data file.Ĭreate a dataset from a simple mathematical expression.įilter data sets based on given criteria. mask expressions and setting internal variables (see for, set, and show commands). There is some support for creating internal loops over e.g. Users can manipulate data sets using mathematical expressions (with some limitations), see 5.2 on page 1↓ for details. 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). In addition, per-residue RMSD can be calculated easily.Īctions that modify coordinates and topology such as the strip/ closest actions can often write an accompanying fully-functional stripped topology file. 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. Trajectory and ensemble reads can be MPI parallelized.Īlmost any file read or written by cpptraj can be compressed (with the exception of the NetCDF trajectory format). 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: