Main Table of Contents

Wed 13 Nov 2013


trjcat concatenates several input trajectory files in sorted order. In case of double time frames the one in the later file is used. By specifying -settime you will be asked for the start time of each file. The input files are taken from the command line, such that a command like trjcat -f *.trr -o fixed.trr should do the trick. Using -cat, you can simply paste several files together without removal of frames with identical time stamps.

One important option is inferred when the output file is amongst the input files. In that case that particular file will be appended to which implies you do not need to store double the amount of data. Obviously the file to append to has to be the one with lowest starting time since one can only append at the end of a file.

If the -demux option is given, the N trajectories that are read, are written in another order as specified in the .xvg file. The .xvg file should contain something like:

0 0 1 2 3 4 5
2 1 0 2 3 5 4

Where the first number is the time, and subsequent numbers point to trajectory indices. The frames corresponding to the numbers present at the first line are collected into the output trajectory. If the number of frames in the trajectory does not match that in the .xvg file then the program tries to be smart. Beware.


-f traj.xtc Input, Mult. Trajectory: xtc trr trj gro g96 pdb cpt
-o trajout.xtc Output, Mult. Trajectory: xtc trr trj gro g96 pdb
-n index.ndx Input, Opt. Index file
-demux remd.xvg Input, Opt. xvgr/xmgr file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-b time -1 First time to use (ps)
-e time -1 Last time to use (ps)
-dt time 0 Only write frame when t MOD dt = first time (ps)
-prec int 3 Precision for .xtc and .gro writing in number of decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]settime bool no Change starting time interactively
-[no]sort bool yes Sort trajectory files (not frames)
-[no]keeplast bool no Keep overlapping frames at end of trajectory
-[no]overwrite bool no Overwrite overlapping frames during appending
-[no]cat bool no Do not discard double time frames