1 .TH g_bundle 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_bundle - analyzes bundles of axes, e.g. helices
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-ol" " bun_len.xvg "
12 .BI "\-od" " bun_dist.xvg "
13 .BI "\-oz" " bun_z.xvg "
14 .BI "\-ot" " bun_tilt.xvg "
15 .BI "\-otr" " bun_tiltr.xvg "
16 .BI "\-otl" " bun_tiltl.xvg "
17 .BI "\-ok" " bun_kink.xvg "
18 .BI "\-okr" " bun_kinkr.xvg "
19 .BI "\-okl" " bun_kinkl.xvg "
20 .BI "\-oa" " axes.pdb "
22 .BI "\-[no]version" ""
32 \&\fB g_bundle\fR analyzes bundles of axes. The axes can be for instance
33 \&helix axes. The program reads two index groups and divides both
34 \&of them in \fB \-na\fR parts. The centers of mass of these parts
35 \&define the tops and bottoms of the axes.
36 \&Several quantities are written to file:
37 \&the axis length, the distance and the z\-shift of the axis mid\-points
38 \&with respect to the average center of all axes, the total tilt,
39 \&the radial tilt and the lateral tilt with respect to the average axis.
43 \&With options \fB \-ok\fR, \fB \-okr\fR and \fB \-okl\fR the total,
44 \&radial and lateral kinks of the axes are plotted. An extra index
45 \&group of kink atoms is required, which is also divided into \fB \-na\fR
46 \&parts. The kink angle is defined as the angle between the kink\-top and
47 \&the bottom\-kink vectors.
51 \&With option \fB \-oa\fR the top, mid (or kink when \fB \-ok\fR is set)
52 \&and bottom points of each axis
53 \&are written to a \fB .pdb\fR file each frame. The residue numbers correspond
54 \&to the axis numbers. When viewing this file with Rasmol, use the
55 \&command line option \fB \-nmrpdb\fR, and type \fB set axis true\fR to
56 \&display the reference axis.
60 Trajectory: xtc trr trj gro g96 pdb cpt
62 .BI "\-s" " topol.tpr"
64 Structure+mass(db): tpr tpb tpa gro g96 pdb
66 .BI "\-n" " index.ndx"
70 .BI "\-ol" " bun_len.xvg"
74 .BI "\-od" " bun_dist.xvg"
78 .BI "\-oz" " bun_z.xvg"
82 .BI "\-ot" " bun_tilt.xvg"
86 .BI "\-otr" " bun_tiltr.xvg"
90 .BI "\-otl" " bun_tiltl.xvg"
94 .BI "\-ok" " bun_kink.xvg"
98 .BI "\-okr" " bun_kinkr.xvg"
102 .BI "\-okl" " bun_kinkl.xvg"
106 .BI "\-oa" " axes.pdb"
108 Protein data bank file
112 Print help info and quit
114 .BI "\-[no]version" "no "
115 Print version info and quit
117 .BI "\-nice" " int" " 19"
120 .BI "\-b" " time" " 0 "
121 First frame (ps) to read from trajectory
123 .BI "\-e" " time" " 0 "
124 Last frame (ps) to read from trajectory
126 .BI "\-dt" " time" " 0 "
127 Only use frame when t MOD dt = first time (ps)
129 .BI "\-tu" " enum" " ps"
130 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
132 .BI "\-xvg" " enum" " xmgrace"
133 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
135 .BI "\-na" " int" " 0"
139 Use the \fI z\fR\-axis as reference instead of the average axis
144 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.