GMX-PRINCIPAL(1) GROMACS GMX-PRINCIPAL(1)

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

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]


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 to specify input files:

Trajectory: xtc trr cpt gro g96 pdb tng
Structure+mass(db): tpr gro g96 pdb brk ent
Index file

Options to specify output files:

xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
-[no]foo (no)
Dummy option to avoid empty array

gmx(1)

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2023, GROMACS development team

October 19, 2023 2023.3