gmx-trjcat(1) GROMACS Manual gmx-trjcat(1)NAMEgmx-trjcat - Concatenate trajectory files
SYNOPSIS
gmx trjcat [-f [<.xtc/.trr/...> [...]]] [-o [<.xtc/.trr/...> [...]]]
[-n [<.ndx>]] [-demux [<.xvg>]] [-nice <int>] [-tu <enum>]
[-xvg <enum>] [-b <time>] [-e <time>] [-dt <time>]
[-[no]vel] [-[no]settime] [-[no]sort] [-[no]keeplast]
[-[no]overwrite] [-[no]cat]
DESCRIPTION
gmx 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 gmx 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. Obvi‐
ously 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.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...> [...]] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-o [<.xtc/.trr/...> [...]] (trajout.xtc) (Output)
Trajectory: xtc trr trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-demux [<.xvg>] (remd.xvg) (Input, Optional)
xvgr/xmgr file
Other options:
-nice <int> (19)
Set the nicelevel
-tu <enum> (ps)
Time unit: fs, ps, ns, us, ms, s
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, 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)
-[no]vel (yes)
Read and write velocities if possible
-[no]settime (no)
Change starting time interactively
-[no]sort (yes)
Sort trajectory files (not frames)
-[no]keeplast (no)
Keep overlapping frames at end of trajectory
-[no]overwrite (no)
Overwrite overlapping frames during appending
-[no]cat (no)
Do not discard double time frames
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-trjcat(1)
