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

NAME

6       gmx-bundle - Analyze bundles of axes, e.g., helices
7

SYNOPSIS

9          gmx bundle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                     [-ol [<.xvg>]] [-od [<.xvg>]] [-oz [<.xvg>]]
11                     [-ot [<.xvg>]] [-otr [<.xvg>]] [-otl [<.xvg>]]
12                     [-ok [<.xvg>]] [-okr [<.xvg>]] [-okl [<.xvg>]]
13                     [-oa [<.pdb>]] [-b <time>] [-e <time>] [-dt <time>]
14                     [-tu <enum>] [-xvg <enum>] [-na <int>] [-[no]z]
15

DESCRIPTION

17       gmx bundle analyzes bundles of axes. The axes can be for instance helix
18       axes. The program reads two index groups and divides both  of  them  in
19       -na  parts. The centers of mass of these parts define the tops and bot‐
20       toms of the axes.  Several quantities are written  to  file:  the  axis
21       length,  the  distance  and  the  z-shift  of  the axis mid-points with
22       respect to the average center of all axes, the total tilt,  the  radial
23       tilt and the lateral tilt with respect to the average axis.
24
25       With  options -ok, -okr and -okl the total, radial and lateral kinks of
26       the axes are plotted. An extra index group of kink atoms  is  required,
27       which  is also divided into -na parts. The kink angle is defined as the
28       angle between the kink-top and the bottom-kink vectors.
29
30       With option -oa the top, mid (or kink  when  -ok  is  set)  and  bottom
31       points  of each axis are written to a .pdb file each frame. The residue
32       numbers correspond to the axis numbers. When  viewing  this  file  with
33       Rasmol,  use the command line option -nmrpdb, and type set axis true to
34       display the reference axis.
35

OPTIONS

37       Options to specify input files:
38
39       -f [<.xtc/.trr/…>] (traj.xtc)
40              Trajectory: xtc trr cpt gro g96 pdb tng
41
42       -s [<.tpr/.gro/…>] (topol.tpr)
43              Structure+mass(db): tpr gro g96 pdb brk ent
44
45       -n [<.ndx>] (index.ndx) (Optional)
46              Index file
47
48       Options to specify output files:
49
50       -ol [<.xvg>] (bun_len.xvg)
51              xvgr/xmgr file
52
53       -od [<.xvg>] (bun_dist.xvg)
54              xvgr/xmgr file
55
56       -oz [<.xvg>] (bun_z.xvg)
57              xvgr/xmgr file
58
59       -ot [<.xvg>] (bun_tilt.xvg)
60              xvgr/xmgr file
61
62       -otr [<.xvg>] (bun_tiltr.xvg)
63              xvgr/xmgr file
64
65       -otl [<.xvg>] (bun_tiltl.xvg)
66              xvgr/xmgr file
67
68       -ok [<.xvg>] (bun_kink.xvg) (Optional)
69              xvgr/xmgr file
70
71       -okr [<.xvg>] (bun_kinkr.xvg) (Optional)
72              xvgr/xmgr file
73
74       -okl [<.xvg>] (bun_kinkl.xvg) (Optional)
75              xvgr/xmgr file
76
77       -oa [<.pdb>] (axes.pdb) (Optional)
78              Protein data bank file
79
80       Other options:
81
82       -b <time> (0)
83              Time of first frame to read from trajectory (default unit ps)
84
85       -e <time> (0)
86              Time of last frame to read from trajectory (default unit ps)
87
88       -dt <time> (0)
89              Only use frame when t MOD dt = first time (default unit ps)
90
91       -tu <enum> (ps)
92              Unit for time values: fs, ps, ns, us, ms, s
93
94       -xvg <enum> (xmgrace)
95              xvg plot formatting: xmgrace, xmgr, none
96
97       -na <int> (0)
98              Number of axes
99
100       -[no]z (no)
101              Use the z-axis as reference instead of the average axis
102

SEE ALSO

104       gmx(1)
105
106       More    information    about    GROMACS    is    available    at     <‐
107       http://www.gromacs.org/>.
108

110       2020, GROMACS development team
111
112
113
114
1152019.6                           Feb 28, 2020                    GMX-BUNDLE(1)
Impressum