.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
trjcat - concatenates trajectory files

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3trjcat\fP
.BI "\-f" " traj.xtc "
.BI "\-o" " trajout.xtc "
.BI "\-n" " index.ndx "
.BI "\-demux" " remd.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-tu" " enum "
.BI "\-xvg" " enum "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-prec" " int "
.BI "\-[no]vel" ""
.BI "\-[no]settime" ""
.BI "\-[no]sort" ""
.BI "\-[no]keeplast" ""
.BI "\-[no]overwrite" ""
.BI "\-[no]cat" ""
.SH DESCRIPTION
\&\fB trjcat\fR concatenates several input trajectory files in sorted order. 
\&In case of double time frames the one in the later file is used. 
\&By specifying \fB \-settime\fR 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 \fB trjcat \-f *.trr \-o fixed.trr\fR should do 
\&the trick. Using \fB \-cat\fR, 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 \fB \-demux\fR option is given, the N trajectories that are
\&read, are written in another order as specified in the \fB .xvg\fR file.
\&The \fB .xvg\fR file should contain something like:


\&\fB 0  0  1  2  3  4  5

\&2  1  0  2  3  5  4\fR

\&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 \fB .xvg\fR file then the program
\&tries to be smart. Beware.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input, Mult.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-o" " trajout.xtc" 
.B Output, Mult.
 Trajectory: xtc trr trj gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-demux" " remd.xvg" 
.B Input, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-b"  " time" " \-1    " 
 First time to use (ps)

.BI "\-e"  " time" " \-1    " 
 Last time to use (ps)

.BI "\-dt"  " time" " 0     " 
 Only write frame when t MOD dt = first time (ps)

.BI "\-prec"  " int" " 3" 
 Precision for \fB .xtc\fR and \fB .gro\fR writing in number of decimal places

.BI "\-[no]vel"  "yes   "
 Read and write velocities if possible

.BI "\-[no]settime"  "no    "
 Change starting time interactively

.BI "\-[no]sort"  "yes   "
 Sort trajectory files (not frames)

.BI "\-[no]keeplast"  "no    "
 Keep overlapping frames at end of trajectory

.BI "\-[no]overwrite"  "no    "
 Overwrite overlapping frames during appending

.BI "\-[no]cat"  "no    "
 Do not discard double time frames

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.