SYNOPSIS

gmx principal [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]

             [-n [<.ndx>]] [-a1 [<.xvg>]] [-a2 [<.xvg>]]
             [-a3 [<.xvg>]] [-om [<.xvg>]] [-nice <int>] [-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 and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)

    Trajectory: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)

    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Input, Optional)

    Index file

-a1 [<.xvg>] (paxis1.xvg) (Output)

    xvgr/xmgr file

-a2 [<.xvg>] (paxis2.xvg) (Output)

    xvgr/xmgr file

-a3 [<.xvg>] (paxis3.xvg) (Output)

    xvgr/xmgr file

-om [<.xvg>] (moi.xvg) (Output)

    xvgr/xmgr file

Other options:

-nice <int> (19)

    Set the nicelevel

-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)

    Time unit: 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

RELATED TO gmx-principal…

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.