Linux Certif

Toute la documentation sur la certification Linux LPI

trjcat

NAME

trjcat - concatenates trajectory files

SYNOPSIS

trjcat -f traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -nice int -tu enum -[no]xvgr -b time -e time -dt time -prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[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 command like trjcat -o fixed.trr *.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.
 Generic trajectory: xtc trr trj gro g96 pdb 

-o trajout.xtc Output, Mult.
 Generic 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 no
 Print help info and quit

-nice int 19
 Set the nicelevel

-tu enum ps
 Time unit:  ps , fs , ns , us , ms , s , m or h

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-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 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]cat no
 do not discard double time frames

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.