GMX-DENSORDER(1)

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

💖 gmx-densorder — Calculate surface fluctuations 💖

okay bestie, welcome to gmx-densorder(1) from the GROMACS manual, aka the glow-up page for when you wanna know exactly where your two phases stop vibing with each other and start a whole new surface situation ✨

🌸 NAME 🌸

gmx-densorder — bestie's fave little tool for calculating surface fluctuations 💅

✨ SYNOPSIS ✨

gmx densorder [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
              [-o [<.dat>]] [-or [<.out> [...]]] [-og [<.xpm> [...]]]
              [-Spect [<.out> [...]]] [-b <time>] [-e <time>]
              [-dt <time>] [-[no]w] [-[no]1d] [-bw <real>]
              [-bwn <real>] [-order <int>] [-axis <string>]
              [-method <enum>] [-d1 <real>] [-d2 <real>]
              [-tblock <int>] [-nlevel <int>]

🫶 DESCRIPTION 🫶

okay so picture this: you ran an MD trajectory, you got a two-phase density distribution, and it's just sitting there along one axis being all... 3D and unbothered. not anymore. 😭

gmx densorder takes that two-phase density distribution along an axis, computed over a MD trajectory, and reduces it to 2D surfaces fluctuating in time — by doing a fit to a functional profile for interfacial densities. it's giving glow-down in the best way possible. iconic. the way that a whole chunky 3D thing becomes cute lil 2D surfaces that wiggle over time? obsessed.

and if you're the kind of girlie who wants the big picture, a time-averaged spatial representation of the interfaces can be output with the option -tavg. 👑

💅 OPTIONS 💅

🎀 Options to specify input files:

  • -s [<.tpr>] (topol.tpr) — Portable xdr run input file. your starting point, the blueprint, the moment before everything pops off.
  • -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory: xtc trr cpt gro g96 pdb tng h5md. all those formats? yeah she eats every single one 🍓
  • -n [<.ndx>] (index.ndx) — Index file. tell her who's who in your system, bestie.

🌈 Options to specify output files:

  • -o [<.dat>] (Density4D.dat) (Optional) — Generic data file. just vibes, just density, just data.
  • -or [<.out> [...]] (hello.out) (Optional) — Generic output file. (yes the default is literally hello.out, we love a friendly queen 🫶)
  • -og [<.xpm> [...]] (interface.xpm) (Optional) — X PixMap compatible matrix file. your interfaces, but make it a picture ✨
  • -Spect [<.out> [...]] (intfspect.out) (Optional) — Generic output file. spectra girlies rise 🙈

💜 Other options:

  • -b <time> (0) — Time of first frame to read from trajectory (default unit ps). where we start the story, bestie.
  • -e <time> (0) — Time of last frame to read from trajectory (default unit ps). where we put the pen down.
  • -dt <time> (0) — Only use frame when t MOD dt = first time (default unit ps). not every frame makes the cut. it's giving selective. 💀
  • -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files. turn it on and she SHOWS you her work.
  • -[no]1d (no) — Pseudo-1d interface geometry. the lil pretend-1D version, lowkey cute.
  • -bw <real> (0.2) — Binwidth of density distribution tangential to interface.
  • -bwn <real> (0.05) — Binwidth of density distribution normal to interface.
  • -order <int> (0) — Order of Gaussian filter, order 0 equates to NO filtering. zero means zero, no filter, no cap.
  • -axis <string> (Z) — Axis Direction - X, Y or Z. pick your main character axis 👑
  • -method <enum> (bisect) — Interface location method: bisect, functional. two methods, two girls, both valid.
  • -d1 <real> (0) — Bulk density phase 1 (at small z).
  • -d2 <real> (1000) — Bulk density phase 2 (at large z).
  • -tblock <int> (100) — Number of frames in one time-block average.
  • -nlevel <int> (100) — Number of Height levels in 2D - XPixMaps. so many levels. so many pixels. so much slay ✨
ngl bestie, -bw, -bwn, -d1, -d2 and -tblock are doing a lot of heavy lifting for your interface shape — set them with intention, not with chaos. 🧚

🔥 SEE ALSO 🔥

  • gmx(1) — the mothership, the main character, go read her next.

More information about GROMACS is available at <http://www.gromacs.org/>. fr fr, go look, iykyk 🌐

2026, GROMACS development team — protect them at all costs, they gave us this whole thing 🫶

okay and that's the whole page bestie!! this was GROMACS 2026.4, dropped Oct 02, 2026, and she is sexy, she is free, she is GMX-DENSORDER(1) 💅✨ no cap, go order some densities. periodt. 💖

📦 where this page comes from