GMX-ORDER(1)

📦
version 2026.4 · 8 versions
, in nixpkgs unstable, ubuntu stonking

✨ GMX-ORDER(1) ✨

okay bestie, welcome to the gmx-order page 💖 this is part of GROMACS (the whole gmx fam, iykyk), and it's the one that does order parameters per atom for carbon tails. buckle up, she's a niche queen but she SERVES 🫶

🌸 NAME 🌸

gmx-order — compute the order parameter per atom for carbon tails 💅

🎀 SYNOPSIS 🎀

gmx order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nr [<.ndx>]]
          [-s [<.tpr>]] [-o [<.xvg>]] [-od [<.xvg>]] [-ob [<.pdb>]]
          [-os [<.xvg>]] [-Sg [<.xvg>]] [-Sk [<.xvg>]]
          [-Sgsl [<.xvg>]] [-Sksl [<.xvg>]] [-b <time>] [-e <time>]
          [-dt <time>] [-[no]w] [-xvg <enum>] [-d <enum>] [-sl <int>]
          [-[no]szonly] [-[no]permolecule] [-[no]radial]
          [-[no]calcdist]

🦋 DESCRIPTION 🦋

so gmx order computes the order parameter per atom for carbon tails, literally that's her whole job. for atom i, the vector i-1, i+1 gets used, together with an axis. 📐

the index file should contain only the groups you're actually using for calculations — each group of equivalent carbons along the relevant acyl chain goes in its own group. and no generic groups (like System, Protein) in the index file please, because that confuses the program 🥴 (not that it matters for tetrahedral order parameters tho, those only work for water anyway 💧).

gmx order can also hand you all diagonal elements of the order tensor, and it can even calculate the deuterium order parameter Scd (which is the default). here's the tea:

  • if you pass -szonly, you get only one order tensor component (the one you pick with -d), and the order parameter per slice also gets calculated ✨
  • if -szonly is not selected, you get all the diagonal elements and the deuterium order parameter.

the tetrahedrality order parameters can be determined around an atom, and both angle and distance order parameters are calculated. for the full lore, go read P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. 📚

⭐ OPTIONS ⭐

💾 Options to specify input files

  • -f [<.xtc/.trr/...>] (default traj.xtc) — the trajectory, hun. formats: xtc trr cpt gro g96 pdb tng h5md
  • -n [<.ndx>] (default index.ndx) — Index file
  • -nr [<.ndx>] (default index.ndx) (Optional) — Index file
  • -s [<.tpr>] (default topol.tpr) — Portable xdr run input file

📝 Options to specify output files

  • -o [<.xvg>] (default order.xvg) — xvgr/xmgr file
  • -od [<.xvg>] (default deuter.xvg) — xvgr/xmgr file
  • -ob [<.pdb>] (default eiwit.pdb) (Optional) — Protein data bank file
  • -os [<.xvg>] (default sliced.xvg) — xvgr/xmgr file
  • -Sg [<.xvg>] (default sg-ang.xvg) (Optional) — xvgr/xmgr file
  • -Sk [<.xvg>] (default sk-dist.xvg) (Optional) — xvgr/xmgr file
  • -Sgsl [<.xvg>] (default sg-ang-slice.xvg) (Optional) — xvgr/xmgr file
  • -Sksl [<.xvg>] (default sk-dist-slice.xvg) (Optional) — xvgr/xmgr file

🌈 Other options

  • -b <time> (default 0) — Time of first frame to read from trajectory (default unit ps)
  • -e <time> (default 0) — Time of last frame to read from trajectory (default unit ps)
  • -dt <time> (default 0) — Only use frame when t MOD dt = first time (default unit ps)
  • -[no]w (default no) — View output .xvg, .xpm, .eps and .pdb files 👀
  • -xvg <enum> (default xmgrace) — xvg plot formatting: xmgrace, xmgr, none
  • -d <enum> (default z) — Direction of the normal on the membrane: z, x, y
  • -sl <int> (default 1) — Calculate order parameter as function of box length, dividing the box into this number of slices 🍰
  • -[no]szonly (default no) — Only give Sz element of order tensor. (axis can be specified with -d)
  • -[no]permolecule (default no) — Compute per-molecule Scd order parameters
  • -[no]radial (default no) — Compute a radial membrane normal
  • -[no]calcdist (default no) — Compute distance from a reference

💀 KNOWN ISSUES 💀

  • This tool only works for saturated carbons and united atom force fields. For anything else, it is highly recommended to use a different analysis method! no cap, do not try to make her do something she can't 🚫
  • The option -unsat claimed to do analysis for unsaturated carbons but this hasn't worked ever since it was added and has thus been removed. rip -unsat, you never once functioned 😭
fr fr, read the known issues before you @ her. she's a specialized girlie and she knows it.

🔥 SEE ALSO 🔥

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

2026, GROMACS development team

okay that's the whole page bestie, you ate 💅✨ — this was GROMACS 2026.4, dated Oct 02, 2026, and it's the GMX-ORDER(1) era of the manpage. now go compute those carbon tail order parameters, main character energy only 🦋🍓🧚💜

📦 where this page comes from