In CPPTRAJ, Actions and Analyses can generate one or more data sets which are available for further processing. For example, the distance command creates a data set containing distances vs time. The data set can be named by the user simply by specifying a non-keyword string as an additional argument. If no name is given, a default one will be generated based on the action name and data set number. For example:
distance d1-2 :1 :2 out d1-2.dat
will create a data set named “d1-2”. If a name is not specified, e.g.:
distance :1 :2 out d1-2.dat
the data set will be named “Dis_00000”.
Data files are created automatically by most commands, usually via the “out” keyword. Data files can also be explicitly created with the write/writedata and create commands. Data can also be read in from files via the readdata command. Cpptraj currently recognizes the formats listed in the table below, although it cannot write in all formats. In addition, a data set must be valid for the data file format. For example, 3D data (such as a grid) can be written to an OpenDX format file but not a Grace format file.
The default file format is called ’Standard’, which simply has data in columns, like ptraj, although multiple data sets can be directed to the same output file. The format of a file can be changed either by specifying a recognized keyword (either on the command line itself or later via a ’datafile’ command) or by giving the file an extension corresponding to the format, so ’filename.agr’ will output in Grace format, and ’filename.gnu’ will output in Gnuplot contour, and so on. The xmgrace/gnuplot output is particularly nice for the secstruct sumout and rmsd perresout files. Additional options for data files can be found in the Data File Options section.
Any action using the “out” keyword will allow data sets from separate commands to be written into the same file. For example, the commands:
dihedral phi :1@C :2@N :2@CA :2@C out phipsi.dat dihedral psi :2@N :2@CA :2@C :3@N out phipsi.dat
will assign the “phi” and “psi” data sets generated from each action to the standard data output file “phipsi.dat”:
#Frame phi psi
|DataFile formats recognized by CPPTRAJ. ’Valid Dimensions’ shows what dimensions the format is valid for (e.g. you cannot write a 1D data set with OpenDX format).|
|Format||Filename Extensions||Keyword||Valid Dimensions||Notes|
|Standard||.dat||dat||1D, 2D, 3D|
|Amber REM log||.log||remlog||–||Read Only.|
|Amber MDOUT||.mdout||mdout||–||Energy information, Read Only.|
|Amber Evecs||.evecs||evecs||Modes data set only|
|Amber Constant pH output||.cpout||cpout||pH data only|
|Density Peaks||.peaks||peaks||3D density peaks (spam/volmap)|
|Vector pseudo-traj||.vectraj||vectraj||Vector data set only||Write Only.|
|Gromacs XVG||.xvg||xvg||–||Read Only.|
|Charmm REPD log||.exch||charmmrepd||–||Read Only.|
|Pairwise Cache (binary)||.cmatrix||cmatrix||pairwise distances||Used for cluster analysis.|
|Pairwise Cache (NetCDF)||.nccmatrix||nccmatris||pairwise distances||Used for cluster analysis.|