GMX-PRINCIPAL(1) GROMACS GMX-PRINCIPAL(1) 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 h5md -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 SEE ALSO gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>. COPYRIGHT 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-PRINCIPAL(1)
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