gmx bundle¶
Synopsis¶
gmx bundle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-ol [<.xvg>]] [-od [<.xvg>]] [-oz [<.xvg>]]
[-ot [<.xvg>]] [-otr [<.xvg>]] [-otl [<.xvg>]]
[-ok [<.xvg>]] [-okr [<.xvg>]] [-okl [<.xvg>]]
[-oa [<.pdb>]] [-b <time>] [-e <time>] [-dt <time>]
[-tu <enum>] [-xvg <enum>] [-na <int>] [-[no]z]
Description¶
gmx bundle analyzes bundles of axes. The axes can be for instance
helix axes. The program reads two index groups and divides both
of them in -na 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 -ok, -okr and -okl 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 -na
parts. The kink angle is defined as the angle between the kink-top and
the bottom-kink vectors.
With option -oa the top, mid (or kink when -ok is set)
and bottom points of each axis
are written to a .pdb file each frame. The residue numbers correspond
to the axis numbers. When viewing this file with Rasmol, use the
command line option -nmrpdb, and type set axis true to
display the reference axis.
Options¶
Options to specify input files:
-f[<.xtc/.trr/…>] (traj.xtc)- Trajectory: xtc trr cpt gro g96 pdb tng
-s[<.tpr/.gro/…>] (topol.tpr)- Structure+mass(db): tpr gro g96 pdb brk ent
-n[<.ndx>] (index.ndx) (Optional)- Index file
Options to specify output files:
-ol[<.xvg>] (bun_len.xvg)- xvgr/xmgr file
-od[<.xvg>] (bun_dist.xvg)- xvgr/xmgr file
-oz[<.xvg>] (bun_z.xvg)- xvgr/xmgr file
-ot[<.xvg>] (bun_tilt.xvg)- xvgr/xmgr file
-otr[<.xvg>] (bun_tiltr.xvg)- xvgr/xmgr file
-otl[<.xvg>] (bun_tiltl.xvg)- xvgr/xmgr file
-ok[<.xvg>] (bun_kink.xvg) (Optional)- xvgr/xmgr file
-okr[<.xvg>] (bun_kinkr.xvg) (Optional)- xvgr/xmgr file
-okl[<.xvg>] (bun_kinkl.xvg) (Optional)- xvgr/xmgr file
-oa[<.pdb>] (axes.pdb) (Optional)- Protein data bank file
Other options:
-b<time> (0)- Time of first frame to read from trajectory (default unit ps)
-e<time> (0)- Time of last frame to read from trajectory (default unit ps)
-dt<time> (0)- Only use frame when t MOD dt = first time (default unit ps)
-tu<enum> (ps)- Unit for time values: fs, ps, ns, us, ms, s
-xvg<enum> (xmgrace)- xvg plot formatting: xmgrace, xmgr, none
-na<int> (0)- Number of axes
-[no]z(no)- Use the z-axis as reference instead of the average axis