1trjcat(1)                 GROMACS suite, VERSION 4.5                 trjcat(1)
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NAME

6       trjcat - concatenates trajectory files
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8       VERSION 4.5
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SYNOPSIS

11       trjcat  -f  traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h
12       -[no]version -nice int -tu enum -xvg enum -b  time  -e  time  -dt  time
13       -prec  int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]overwrite
14       -[no]cat
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DESCRIPTION

17       trjcat concatenates several input trajectory files in sorted order.  In
18       case of double time frames the one in the later file is used.  By spec‐
19       ifying  -settime you will be asked for the start time of each file. The
20       input  files  are taken from the command line, such that a command like
21       trjcat -o fixed.trr *.trr should do the trick. Using  -cat you can sim‐
22       ply paste several files together without removal of frames with identi‐
23       cal time stamps.
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26       One important option is inferred when the output file  is  amongst  the
27       input  files.  In  that  case  that particular file will be appended to
28       which implies you do not need to  store  double  the  amount  of  data.
29       Obviously  the file to append to has to be the one with lowest starting
30       time since one can only append at the end of a file.
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33       If the  -demux option is given, the N trajectories that are  read,  are
34       written  in  another  order as specified in the xvg file.  The xvg file
35       should contain something like:
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38       0  0  1  2  3  4  5
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40       2  1  0  2  3  5  4
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42       Where the first number is the time, and  subsequent  numbers  point  to
43       trajectory indices.  The frames corresponding to the numbers present at
44       the first line are collected into the output trajectory. If the  number
45       of  frames  in  the trajectory does not match that in the xvg file then
46       the program tries to be smart. Beware.
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FILES

49       -f traj.xtc Input, Mult.
50        Trajectory: xtc trr trj gro g96 pdb cpt
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52       -o trajout.xtc Output, Mult.
53        Trajectory: xtc trr trj gro g96 pdb
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55       -n index.ndx Input, Opt.
56        Index file
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58       -demux remd.xvg Input, Opt.
59        xvgr/xmgr file
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OTHER OPTIONS

63       -[no]hno
64        Print help info and quit
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66       -[no]versionno
67        Print version info and quit
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69       -nice int 19
70        Set the nicelevel
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72       -tu enum ps
73        Time unit:  fs,  ps,  ns,  us,  ms or  s
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75       -xvg enum xmgrace
76        xvg plot formatting:  xmgrace,  xmgr or  none
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78       -b time -1
79        First time to use (ps)
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81       -e time -1
82        Last time to use (ps)
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84       -dt time 0
85        Only write frame when t MOD dt = first time (ps)
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87       -prec int 3
88        Precision for .xtc and .gro writing in number of decimal places
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90       -[no]velyes
91        Read and write velocities if possible
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93       -[no]settimeno
94        Change starting time interactively
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96       -[no]sortyes
97        Sort trajectory files (not frames)
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99       -[no]keeplastno
100        keep overlapping frames at end of trajectory
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102       -[no]overwriteno
103        overwrite overlapping frames during appending
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105       -[no]catno
106        do not discard double time frames
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SEE ALSO

110       gromacs(7)
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112       More  information  about  GROMACS  is  available  at   <http://www.gro‐
113       macs.org/>.
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117                                Thu 26 Aug 2010                      trjcat(1)
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