gmx principal
Synopsis
gmx principal [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
[-n [<.ndx>]] [-a1 [<.xvg>]] [-a2 [<.xvg>]]
[-a3 [<.xvg>]] [-om [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
[-[no]foo]
Description
gmx principal calculates the three principal axes of inertia for a group
of atoms. NOTE: Old versions of GROMACS wrote the output data in a
strange transposed way. As of GROMACS 5.0, the output file paxis1.dat
contains the x/y/z components of the first (major) principal axis for
each frame, and similarly for the middle and minor axes in paxis2.dat
and paxis3.dat.
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:
- -a1 [<.xvg>] (paxis1.xvg)
- xvgr/xmgr file
- -a2 [<.xvg>] (paxis2.xvg)
- xvgr/xmgr file
- -a3 [<.xvg>] (paxis3.xvg)
- xvgr/xmgr file
- -om [<.xvg>] (moi.xvg)
- xvgr/xmgr file
Other options:
- -b <time> (0)
- First frame (ps) to read from trajectory
- -e <time> (0)
- Last frame (ps) to read from trajectory
- -dt <time> (0)
- Only use frame when t MOD dt = first time (ps)
- -tu <enum> (ps)
- Unit for time values: fs, ps, ns, us, ms, s
- -[no]w (no)
- View output .xvg, .xpm, .eps and .pdb files
- -xvg <enum>
- xvg plot formatting: xmgrace, xmgr, none
- -[no]foo (no)
- Dummy option to avoid empty array