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

NAME

6       gmx-view - View a trajectory on an X-Windows terminal
7

SYNOPSIS

9          gmx view [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]] [-b <time>]
10                   [-e <time>] [-dt <time>]
11

DESCRIPTION

13       gmx view is the GROMACS trajectory viewer. This program reads a trajec‐
14       tory file, a run input file and an index file and plots a 3D  structure
15       of  your  molecule on your standard X Window screen. No need for a high
16       end graphics workstation, it even works on Monochrome screens.
17
18       The following features have been implemented: 3D view, rotation, trans‐
19       lation  and  scaling of your molecule(s), labels on atoms, animation of
20       trajectories, hardcopy in PostScript format, user defined  atom-filters
21       runs  on  MIT-X  (real X), open windows and motif, user friendly menus,
22       option to remove periodicity, option to show computational box.
23
24       Some of the more common X command line options can be  used:  -bg,  -fg
25       change colors, -font fontname changes the font.
26

OPTIONS

28       Options to specify input files:
29
30       -f [<.xtc/.trr/…>] (traj.xtc)
31              Trajectory: xtc trr cpt gro g96 pdb tng
32
33       -s [<.tpr>] (topol.tpr)
34              Portable xdr run input file
35
36       -n [<.ndx>] (index.ndx) (Optional)
37              Index file
38
39       Other options:
40
41       -b <time> (0)
42              Time of first frame to read from trajectory (default unit ps)
43
44       -e <time> (0)
45              Time of last frame to read from trajectory (default unit ps)
46
47       -dt <time> (0)
48              Only use frame when t MOD dt = first time (default unit ps)
49

KNOWN ISSUES

51       · Balls option does not work
52
53       · Some times dumps core without a good reason
54

SEE ALSO

56       gmx(1)
57
58       More     information    about    GROMACS    is    available    at    <‐
59       http://www.gromacs.org/>.
60

62       2019, GROMACS development team
63
64
65
66
672019.4                           Oct 02, 2019                      GMX-VIEW(1)
Impressum