trjcat(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c trjcat(1)
NAME
trjcat - concatenates trajectory files
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
trjcat -f traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -[no]version -nice int -tu enum -xvg enum -b time -e time -dt time
-prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]overwrite -[no]cat
DESCRIPTION
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 com-
mand 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.
FILES
-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]hno
Print help info and quit
-[no]versionno
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]velyes
Read and write velocities if possible
-[no]settimeno
Change starting time interactively
-[no]sortyes
Sort trajectory files (not frames)
-[no]keeplastno
Keep overlapping frames at end of trajectory
-[no]overwriteno
Overwrite overlapping frames during appending
-[no]catno
Do not discard double time frames
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 trjcat(1)