1GMX-BUNDLE(1)                       GROMACS                      GMX-BUNDLE(1)
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NAME

6       gmx-bundle - Analyze bundles of axes, e.g., helices
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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]
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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 re‐
22       spect to the average center of all axes, the  total  tilt,  the  radial
23       tilt and the lateral tilt with respect to the average axis.
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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.
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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.
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OPTIONS

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

104       gmx(1)
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106       More    information    about    GROMACS    is    available    at     <‐
107       http://www.gromacs.org/>.
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110       2022, GROMACS development team
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1152022.3                           Sep 02, 2022                    GMX-BUNDLE(1)
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