GMX-PRINCIPAL(1)

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version 2026.4 · 8 versions
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✨ GMX-PRINCIPAL(1) — the GROMACS girlies' guide ✨

okay so bestie, welcome to gmx-principal from the GROMACS manual 💖 buckle up, this one's short and sweet and honestly? lowkey iconic.

🌸 NAME 🌸

gmx-principal — calculates the principal axes of inertia for a group of atoms. that's it, that's the whole job 💅

🦋 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 🎀

so gmx principal does one thing and does it gorgeously: it calculates the three principal axes of inertia for a group of atoms. main character energy fr fr 🫶

NOTE ⚠️ and this part matters, bestie: 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. so if you're out here reading ancient output files and nothing makes sense... that's why. not you, it's the transposed data 😭

💖 OPTIONS 💖

✨ Options to specify input files ✨

  • -f [<.xtc/.trr/...>] (default traj.xtc) — the trajectory, bestie. accepts xtc trr cpt gro g96 pdb tng h5md 🍓
  • -s [<.tpr/.gro/...>] (default topol.tpr) — structure + mass(db). accepts tpr gro g96 pdb brk ent 🧚
  • -n [<.ndx>] (default index.ndx) — index file. Optional, so no pressure 💜

✨ Options to specify output files ✨

  • -a1 [<.xvg>] (default paxis1.xvg) — xvgr/xmgr file 🌸
  • -a2 [<.xvg>] (default paxis2.xvg) — xvgr/xmgr file 🌸
  • -a3 [<.xvg>] (default paxis3.xvg) — xvgr/xmgr file 🌸
  • -om [<.xvg>] (default moi.xvg) — xvgr/xmgr file 🌸

✨ Other options ✨

  • -b <time> (default 0) — time of the first frame to read from the trajectory (default unit is ps) ⏰
  • -e <time> (default 0) — time of the last frame to read from the trajectory (default unit is ps) ⏰
  • -dt <time> (default 0) — only use a frame when t MOD dt = first time (default unit is ps) ⏰
  • -tu <enum> (default ps) — unit for time values: fs, ps, ns, us, ms, s 🕰️
  • -[no]w (default no) — view output .xvg, .xpm, .eps and .pdb files 👀
  • -xvg <enum> (default xmgrace) — xvg plot formatting: xmgrace, xmgr, none 📊
  • -[no]foo (default no) — dummy option to avoid an empty array 💀 yeah. it's literally just there so the array isn't empty. no notes. slay, i guess 👑

🌈 SEE ALSO 🌈

more info about GROMACS lives at <http://www.gromacs.org/> — go peek, iykyk 🦋

2026, GROMACS development team 💜

and that's the whole page, bestie!! 🎀 this was GROMACS 2026.4, dated Oct 02, 2026, and remember: same manual, same facts, just with way more sparkle ✨ mwah 💅🫶

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