GMX-DYECOUPL(1)

✨ GMX-DYECOUPL(1) ✨

okay bestie, welcome to the GROMACS manual page for gmx-dyecoupl, and no cap, this one is kinda niche but so fun once you get it 💅

---

🌸 NAME 🌸

gmx-dyecoupl — pull the dye dynamics out of your trajectories, fr fr 🎀

---

💖 SYNOPSIS 💖

gmx dyecoupl [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-ot [<.xvg>]]
             [-oe [<.xvg>]] [-o [<.dat>]] [-rhist [<.xvg>]]
             [-khist [<.xvg>]] [-b <time>] [-e <time>] [-tu <enum>]
             [-[no]w] [-xvg <enum>] [-[no]pbcdist] [-[no]norm]
             [-bins <int>] [-R0 <real>]

---

🦋 DESCRIPTION 🦋

So like, gmx dyecoupl extracts dye dynamics from trajectory files. Currently it pulls out R and kappa^2 between your dyes, for (F)RET simulations where we assume dipolar coupling like in the Foerster equation 🧚✨

It also lets you compute R(t) and kappa^2(t), plus R and kappa^2 histograms and averages, and even the instantaneous FRET efficiency E(t) for a Foerster radius you pick with -R0 👑

heads up bestie: your input dyes have to be whole — like, check the res and mol pbc options in trjconv, okay? don't skip that 💀

The dye transition dipole moment needs at least a single atom pair, but ngl you can totally provide multiple atom pairs in the index file. The distance R gets calculated from the COMs of the atom pairs you gave it.

The -pbcdist option computes distances to the nearest periodic image instead of the distance in the box. But plot twist: that only works for periodic boundaries in all 3 dimensions, so don't come for me if it acts up in 2D 🙈

The -norm option (area-)normalizes the histograms. cute, right? 🌈

---

💅 OPTIONS 💅

🫶 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) — your trajectory file, bestie. Formats: xtc trr cpt gro g96 pdb tng h5md 📁
• -n [<.ndx>] (index.ndx) — the index file

🎀 Options to specify output files:

• -ot [<.xvg>] (rkappa.xvg) (Optional) — xvgr/xmgr file ⭐
• -oe [<.xvg>] (insteff.xvg) (Optional) — xvgr/xmgr file ⭐
• -o [<.dat>] (rkappa.dat) (Optional) — generic data file
• -rhist [<.xvg>] (rhist.xvg) (Optional) — xvgr/xmgr file ⭐
• -khist [<.xvg>] (khist.xvg) (Optional) — xvgr/xmgr file ⭐

👑 Other options:

• -b <time> (0) — time of the first frame to read from the trajectory (default unit is ps) ⏰
• -e <time> (0) — time of the last frame to read from the trajectory (default unit is ps) ⏰
• -tu <enum> (ps) — the unit for time values, and your choices are: fs, ps, ns, us, ms, s 🕰️
• -[no]w (no) — view output .xvg, .xpm, .eps and .pdb files 👀
• -xvg <enum> (xmgrace) — xvg plot formatting, pick from: xmgrace, xmgr, none 🎨
• -[no]pbcdist (no) — distance R based on PBC
• -[no]norm (no) — normalize histograms
• -bins <int> (50) — the number of histogram bins 📊
• -R0 <real> (-1) — Foerster radius including kappa^2=2/3 in nm

---

🌟 SEE ALSO 🌟

• gmx(1)

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

---

🌈 COPYRIGHT 🌈

2026, GROMACS development team

---

and that's the whole vibe check, bestie 🫶 go get those dye dynamics, you absolutely ate 💅✨

Version 2026.4 · Oct 02, 2026 · from your GROMACS girls — ily, go slay some trajectories 🎀💜