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

6       g_bundle - analyzes bundles of axes, e.g. helices
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8       VERSION 4.5
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SYNOPSIS

11       g_bundle  -f  traj.xtc  -s  topol.tpr  -n index.ndx -ol bun_len.xvg -od
12       bun_dist.xvg -oz bun_z.xvg -ot  bun_tilt.xvg  -otr  bun_tiltr.xvg  -otl
13       bun_tiltl.xvg  -ok  bun_kink.xvg  -okr bun_kinkr.xvg -okl bun_kinkl.xvg
14       -oa axes.pdb -[no]h -[no]version -nice int -b time -e time -dt time -tu
15       enum -xvg enum -na int -[no]z
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DESCRIPTION

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

41       -f traj.xtc Input
42        Trajectory: xtc trr trj gro g96 pdb cpt
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44       -s topol.tpr Input
45        Structure+mass(db): tpr tpb tpa gro g96 pdb
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47       -n index.ndx Input, Opt.
48        Index file
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50       -ol bun_len.xvg Output
51        xvgr/xmgr file
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53       -od bun_dist.xvg Output
54        xvgr/xmgr file
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56       -oz bun_z.xvg Output
57        xvgr/xmgr file
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59       -ot bun_tilt.xvg Output
60        xvgr/xmgr file
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62       -otr bun_tiltr.xvg Output
63        xvgr/xmgr file
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65       -otl bun_tiltl.xvg Output
66        xvgr/xmgr file
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68       -ok bun_kink.xvg Output, Opt.
69        xvgr/xmgr file
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71       -okr bun_kinkr.xvg Output, Opt.
72        xvgr/xmgr file
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74       -okl bun_kinkl.xvg Output, Opt.
75        xvgr/xmgr file
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77       -oa axes.pdb Output, Opt.
78        Protein data bank file
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OTHER OPTIONS

82       -[no]hno
83        Print help info and quit
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85       -[no]versionno
86        Print version info and quit
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88       -nice int 19
89        Set the nicelevel
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91       -b time 0
92        First frame (ps) to read from trajectory
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94       -e time 0
95        Last frame (ps) to read from trajectory
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97       -dt time 0
98        Only use frame when t MOD dt = first time (ps)
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100       -tu enum ps
101        Time unit:  fs,  ps,  ns,  us,  ms or  s
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103       -xvg enum xmgrace
104        xvg plot formatting:  xmgrace,  xmgr or  none
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106       -na int 0
107        Number of axes
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109       -[no]zno
110        Use the Z-axis as reference iso the average axis
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SEE ALSO

114       gromacs(7)
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116       More   information  about  GROMACS  is  available  at  <http://www.gro‐
117       macs.org/>.
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121                                Thu 26 Aug 2010                    g_bundle(1)
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