.TH gmx-bundle 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices

.SH SYNOPSIS
gmx bundle [\-f [<.xtc/.trr/...>]] [\-s [<.tpr/.tpb/...>]]
           [\-n [<.ndx>]] [\-ol [<.xvg>]] [\-od [<.xvg>]] [\-oz [<.xvg>]]
           [\-ot [<.xvg>]] [\-otr [<.xvg>]] [\-otl [<.xvg>]]
           [\-ok [<.xvg>]] [\-okr [<.xvg>]] [\-okl [<.xvg>]]
           [\-oa [<.pdb>]] [\-nice <int>] [\-b <time>] [\-e <time>]
           [\-dt <time>] [\-tu <enum>] [\-xvg <enum>] [\-na <int>]
           [\-[no]z]

.SH DESCRIPTION
\fBgmx bundle\fR analyzes bundles of axes. The axes can be for instance helix axes. The program reads two index groups and divides both of them in \fB\-na\fR parts. The centers of mass of these parts define the tops and bottoms of the axes. Several quantities are written to file: the axis length, the distance and the z\-shift of the axis mid\-points with respect to the average center of all axes, the total tilt, the radial tilt and the lateral tilt with respect to the average axis.

With options \fB\-ok\fR, \fB\-okr\fR and \fB\-okl\fR the total, radial and lateral kinks of the axes are plotted. An extra index group of kink atoms is required, which is also divided into \fB\-na\fR parts. The kink angle is defined as the angle between the kink\-top and the bottom\-kink vectors.

With option \fB\-oa\fR the top, mid (or kink when \fB\-ok\fR is set) and bottom points of each axis are written to a \fB.pdb\fR file each frame. The residue numbers correspond to the axis numbers. When viewing this file with Rasmol, use the command line option \fB\-nmrpdb\fR, and type \fBset axis true\fR to display the reference axis.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-ol" " [<.xvg>] (bun_len.xvg) (Output)"
    xvgr/xmgr file

.BI "\-od" " [<.xvg>] (bun_dist.xvg) (Output)"
    xvgr/xmgr file

.BI "\-oz" " [<.xvg>] (bun_z.xvg) (Output)"
    xvgr/xmgr file

.BI "\-ot" " [<.xvg>] (bun_tilt.xvg) (Output)"
    xvgr/xmgr file

.BI "\-otr" " [<.xvg>] (bun_tiltr.xvg) (Output)"
    xvgr/xmgr file

.BI "\-otl" " [<.xvg>] (bun_tiltl.xvg) (Output)"
    xvgr/xmgr file

.BI "\-ok" " [<.xvg>] (bun_kink.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-okr" " [<.xvg>] (bun_kinkr.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-okl" " [<.xvg>] (bun_kinkl.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-oa" " [<.pdb>] (axes.pdb) (Output, Optional)"
    Protein data bank file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-tu" " <enum> (ps)"
    Time unit: fs, ps, ns, us, ms, s

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-na" " <int> (0)"
    Number of axes

.BI "\-[no]z" "  (no)"
    Use the \fIz\fR\-axis as reference instead of the average axis


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.