1GMX-TRJCAT(1)                       GROMACS                      GMX-TRJCAT(1)
2
3
4

NAME

6       gmx-trjcat - Concatenate trajectory files
7

SYNOPSIS

9          gmx trjcat [-f [<.xtc/.trr/...> [...]]] [-n [<.ndx>]] [-demux [<.xvg>]]
10                     [-o [<.xtc/.trr/...> [...]]] [-tu <enum>] [-xvg <enum>]
11                     [-b <time>] [-e <time>] [-dt <time>] [-[no]settime]
12                     [-[no]sort] [-[no]keeplast] [-[no]overwrite] [-[no]cat]
13

DESCRIPTION

15       gmx trjcat concatenates several input trajectory files in sorted order.
16       In case of double time frames the one in the later file  is  used.   By
17       specifying  -settime you will be asked for the start time of each file.
18       The input files are taken from the command line, such  that  a  command
19       like  gmx trjcat -f *.trr -o fixed.trr should do the trick. Using -cat,
20       you can simply paste several files together without removal  of  frames
21       with identical time stamps.
22
23       One  important  option  is inferred when the output file is amongst the
24       input files. In that case that particular  file  will  be  appended  to
25       which  implies you do not need to store double the amount of data.  Ob‐
26       viously the file to append to has to be the one  with  lowest  starting
27       time since one can only append at the end of a file.
28
29       If  the  -demux  option is given, the N trajectories that are read, are
30       written in another order as specified in the .xvg file.  The .xvg  file
31       should contain something like:
32
33          0  0  1  2  3  4  5
34          2  1  0  2  3  5  4
35
36       The  first  number is the time, and subsequent numbers point to trajec‐
37       tory indices.  The frames corresponding to the numbers present  at  the
38       first  line  are collected into the output trajectory. If the number of
39       frames in the trajectory does not match that in the .xvg file then  the
40       program tries to be smart. Beware.
41

OPTIONS

43       Options to specify input files:
44
45       -f [<.xtc/.trr/...> [...]] (traj.xtc)
46              Trajectory: xtc trr cpt gro g96 pdb tng
47
48       -n [<.ndx>] (index.ndx) (Optional)
49              Index file
50
51       -demux [<.xvg>] (remd.xvg) (Optional)
52              xvgr/xmgr file
53
54       Options to specify output files:
55
56       -o [<.xtc/.trr/...> [...]] (trajout.xtc)
57              Trajectory: xtc trr gro g96 pdb tng
58
59       Other options:
60
61       -tu <enum> (ps)
62              Unit for time values: fs, ps, ns, us, ms, s
63
64       -xvg <enum> (xmgrace)
65              xvg plot formatting: xmgrace, xmgr, none
66
67       -b <time> (-1)
68              First time to use (ps)
69
70       -e <time> (-1)
71              Last time to use (ps)
72
73       -dt <time> (0)
74              Only write frame when t MOD dt = first time (ps)
75
76       -[no]settime (no)
77              Change starting time interactively
78
79       -[no]sort (yes)
80              Sort trajectory files (not frames)
81
82       -[no]keeplast (no)
83              Keep overlapping frames at end of trajectory
84
85       -[no]overwrite (no)
86              Overwrite overlapping frames during appending
87
88       -[no]cat (no)
89              Do not discard double time frames
90

SEE ALSO

92       gmx(1)
93
94       More     information    about    GROMACS    is    available    at    <‐
95       http://www.gromacs.org/>.
96

98       2022, GROMACS development team
99
100
101
102
1032022.2                           Jun 16, 2022                    GMX-TRJCAT(1)
Impressum