GMX-SORIENT(1)

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

💖 gmx-sorient 💖

okay bestie, welcome to the GROMACS manual page for gmx-sorient — yes that's the whole name, we're analyzing solvent orientation around solutes and we ARE going to slay it ✨

✨ NAME ✨

gmx-sorient — analyze solvent orientation around solutes 🌸

🎀 SYNOPSIS 🎀

gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]]
            [-co [<.xvg>]] [-rc [<.xvg>]] [-b <time>] [-e <time>]
            [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]com] [-[no]v23]
            [-rmin <real>] [-rmax <real>] [-cbin <real>]
            [-rbin <real>] [-[no]pbc]

💅 DESCRIPTION 💅

so, gmx sorient looks at how the solvent molecules are oriented around your solutes. the way it does this: it takes the vector from one or more reference positions to the first atom of each solvent molecule, and then it calculates two angles off of that. two. angles. periodt.

  • theta_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3 🦋
  • theta_2: the angle with the normal of the solvent plane — and that plane is defined by the same three atoms — or, when the option -v23 is set, the angle with the vector between atoms 2 and 3 🌈

so the reference can be either a set of atoms, or the center of mass of a set of atoms, your choice bestie. and the group of solvent atoms should consist of 3 atoms per solvent molecule (three, not two, not four, three 💀). also!! only the solvent molecules sitting between -rmin and -rmax are considered for -o and -no, every single frame. no exceptions.

here's the breakdown of what each output actually gives, because i know you want the details:

  • -o: distribution of cos(theta_1) for rmin<=r<=rmax.
  • -no: distribution of cos(theta_2) for rmin<=r<=rmax.
  • -ro: <cos(theta_1)> and <3cos(^2theta_2)-1> as a function of the distance.
  • -co: the sum over all solvent molecules within distance r of cos(theta_1) and 3cos(^2(theta_2)-1) as a function of r.
  • -rc: the distribution of the solvent molecules as a function of r

🌸 OPTIONS 🌸

💖 Options to specify input files 💖

  • -f [<.xtc/.trr/...>] (default traj.xtc) — the trajectory, obviously 💫 and the formats it'll eat are: xtc trr cpt gro g96 pdb tng h5md
  • -s [<.tpr/.gro/...>] (default topol.tpr) — structure+mass(db), the whole vibe: tpr gro g96 pdb brk ent
  • -n [<.ndx>] (default index.ndx) (Optional) — index file, only if you want it boo 🎀

🦋 Options to specify output files 🦋

  • -o [<.xvg>] (default sori.xvg) — xvgr/xmgr file ✨
  • -no [<.xvg>] (default snor.xvg) — xvgr/xmgr file ✨
  • -ro [<.xvg>] (default sord.xvg) — xvgr/xmgr file ✨
  • -co [<.xvg>] (default scum.xvg) — xvgr/xmgr file ✨
  • -rc [<.xvg>] (default scount.xvg) — xvgr/xmgr file ✨

👑 Other options 👑

  • -b <time> (default 0) — time of first frame to read from the trajectory (default unit is ps) ⏰
  • -e <time> (default 0) — time of 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) ⏰
  • -[no]w (default no) — view the output .xvg, .xpm, .eps and .pdb files 👀
  • -xvg <enum> (default xmgrace) — xvg plot formatting, and your options are: xmgrace, xmgr, none 🎨
  • -[no]com (default no) — use the center of mass as the reference position 🫶
  • -[no]v23 (default no) — use the vector between atoms 2 and 3 🌈
  • -rmin <real> (default 0) — minimum distance (in nm) 📏
  • -rmax <real> (default 0.5) — maximum distance (in nm) 📏
  • -cbin <real> (default 0.02) — binwidth for the cosine 📊
  • -rbin <real> (default 0.02) — binwidth for r (in nm) 📊
  • -[no]pbc (default no) — check PBC for the center of mass calculation. this one's only necessary when your reference group consists of several molecules, so don't stress if it's just the one 💜

🔥 SEE ALSO 🔥

2026, GROMACS development team

okay that's the whole thing, you're officially a solvent-orientation girlie now 🧚 no cap. this was GROMACS 2026.4, dated Oct 02, 2026 — love you, go analyze something iconic 💖✨👑

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