NAME

gmx-principal - Calculate principal axes of inertia for a group of atoms

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): 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
-[no]w (no): View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace): xvg plot formatting: xmgrace, xmgr, none
-[no]foo (no): Dummy option to avoid empty array

COPYRIGHT

2025, GROMACS development team

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