Data File Options

Data file output can be handled in multiple ways in CPPTRAJ.

Output data files can be created by Actions/Analyses/Commands, or can be explicitly created with writedata or create commands. Reading data from files is only done via the readdata command. In general, data files which have been declared with an out keyword will recognize data file write keywords on the same command line.

For example, the time argument can be passed directly to the output from a distance command:

 distance d0 :1 :2 out d0.agr time 0.001

The data file format can be changed from standard implicitly by using specific filename extensions or keywords. If the extension is not recognized or no keyword is give the default format is ’Standard’. Keywords and extensions for data file formats recognized by CPPTRAJ are shown here. Note that the use of certain options may be restricted for certain data file formats. These options can also be passed to data files via the datafile command.

[<format keyword>]
[{xlabel|ylabel|zlabel} <label>] [{xmin|ymin|zmin} <min>] [sort]  {xstep|ystep|zstep} <step>] [time <dt>] [prec <width>[.<precision>]]
[xprec <width>[.<precision>]] [xfmt {double|scientific|general}]

{xlabel | ylabel | zlabel} <label> Set the x-axis label for the specified datafile to <label>. For regular data files this is the header for the first column of data. If the data is at least 2-dimensional ’datafile ylabel <label>’ will likewise set the y-axis label.
{xmin | ymin | zmin} <min> Set the starting X coordinate value to <min>. If the data is at least 2-dimensional ’datafile ymin <min>’ will likewise set the starting Y coordinate value.
sort Sort data sets prior to write. Ordering is by name, aspect, then index (all descending).
{xstep | ystep | zstep} <step> Multiply each frame number by <step> (x coordinates). If the data is at least 2-dimensional ’datafile ystep <step>’ will likewise multiply y coordinates by <step>.
time <dt> Equivalent to the ptraj argument ’time’ that could be specified with many actions. Multiplies frame numbers (x-axis) by <dt>.
prec <width>[<precision>] Change the output format width (and optionally precision) of all sets subsequently added to the data file (i.e. does not change the precision of any data sets currently in the file). For example, prec 12.4, prec 10
xprec <width>[<precision>] Change output ordinate width and precision.
xfmt {double|scientific|general} Change output ordinate format.
[noensextension] Omit ensemble extension in ensemble processing mode. NOTE: THIS OPTION HAS NOT BEEN FULLY TESTED IN PARALLEL.

Standard Data File Options
Grace Data File Options
Gnuplot Data File Options
Amber REM Log Options
Amber MDOUT Options
Evecs File Options
Vector pseudo-traj Options
OpenDX file options
CCP4 file options
Amber Constant pH Out options