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> (xmgrace)

xvg plot formatting: xmgrace, xmgr, none

-[no]foo (no)

Dummy option to avoid empty array