Man page - gmx-principal(1)
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- gmx-trjcat(1)
- gmx-confrms(1)
- gmx_d(1)
- gmx-xpm2ps(1)
- gmx-make_edi(1)
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- gmx-rama(1)
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- gmx-mdmat(1)
- gmx-rotmat(1)
- gmx(1)
- gmx-eneconv(1)
- gmx-h2order(1)
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- gmx-potential(1)
- gmx-wheel(1)
- gmx-mk_angndx(1)
- gmx-x2top(1)
- gmx-genconf(1)
- gmx-mindist(1)
- gmx-dipoles(1)
- gmx-polystat(1)
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- gmx-gyrate-legacy(1)
- gmx-make_ndx(1)
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- xplor2gmx(1)
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- gmx-pdb2gmx(1)
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- gmx-cluster(1)
- gmx-select(1)
- gmx-rmsf(1)
- gmx-angle(1)
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- gmx-disre(1)
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- gmx-tune_pme(1)
- gmx-check(1)
- gmx-nmtraj(1)
- gmx-helix(1)
- gmx-trjorder(1)
- gmx-grompp(1)
- gmx-gangle(1)
- gmx-dssp(1)
- gmx-convert-trj(1)
- gmx-sorient(1)
- gmx-chi(1)
- gmx-anaeig(1)
- gmx-lie(1)
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- gmx-mdrun(1)
- gmx-editconf(1)
- gmx-rdf(1)
- gmx_mpi_d(1)
- gmx-rotacf(1)
- gmx-nmeig(1)
- gmx-gyrate(1)
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Manual
| 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
- -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)
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| May 12, 2025 | 2025.2 |