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gmx-principal(1)                GROMACS Manual                gmx-principal(1)

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

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

SEE ALSO
       gromacs(7)

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

VERSION 5.0.6                                                 gmx-principal(1)