GMX-VELACC(1)

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

💖 GMX-VELACC(1) — the GROMACS girlie's guide 💖

okay so bestie, this is the manual page for gmx-velacc, one of the many little gems that live inside GROMACS 💅 it computes velocity autocorrelation functions, and honestly? it's giving physics main character energy. let's get into it 🦋

✨ NAME ✨

gmx-velacc — no cap, this one just calculates velocity autocorrelation functions 🎀

🌸 SYNOPSIS 🌸

gmx velacc [-f [<.trr/.cpt/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
           [-o [<.xvg>]] [-os [<.xvg>]] [-b <time>] [-e <time>]
           [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]m] [-[no]recip]
           [-[no]mol] [-acflen <int>] [-[no]normalize] [-P <enum>]
           [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]

like look at her. so many flags. so many possibilities 🫶

💜 DESCRIPTION 💜

So gmx velacc computes the velocity autocorrelation function. Periodt. 🔥

And when you hit it with the -m option? It calculates the momentum autocorrelation function instead. Two moods, one tool 💅

Then there's -mol — with this one, you get the velocity autocorrelation function of molecules. Lowkey important detail: in that case your index group should consist of molecule numbers instead of atom numbers. Don't mix them up bestie, iykyk 🙈

Oh and here's the fun part — using -os you can also extract the estimated (vibrational) power spectrum, which is literally the Fourier transform of the velocity autocorrelation function. Iconic. But fr fr, be sure that:

  • your trajectory contains frames with velocity information (i.e. nstvout was set in your original .mdp file) 👑
  • the time interval between data collection points is much shorter than the time scale of the autocorrelation ⭐

that's not optional, that's the vibe check ✅

✨ OPTIONS ✨

🎀 Options to specify input files

  • -f [<.trr/.cpt/...>] (traj.trr) — the Full precision trajectory, she's a whole menu: trr cpt tng h5md 🌈
  • -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — Structure+mass(db), take your pick: tpr gro g96 pdb brk ent 💖
  • -n [<.ndx>] (index.ndx) (Optional) — the Index file, your little list of who's who 📋

🦋 Options to specify output files

  • -o [<.xvg>] (vac.xvg) — an xvgr/xmgr file, this is the moment 💅
  • -os [<.xvg>] (spectrum.xvg) (Optional) — also an xvgr/xmgr file, in case you want the spectrum too 👑

🌸 Other options

  • -b <time> (0) — Time of first frame to read from trajectory (default unit is ps) ⏰
  • -e <time> (0) — Time of last frame to read from trajectory (default unit is ps) ⏰
  • -dt <time> (0) — Only use a frame when t MOD dt = first time (default unit is ps) 🧮
  • -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files 👀
  • -xvg <enum> (xmgrace) — xvg plot formatting, pick your fighter: xmgrace, xmgr, none 🎨
  • -[no]m (no) — Calculate the momentum autocorrelation function 🏃
  • -[no]recip (yes) — Use cm^-1 on the X-axis instead of 1/ps for spectra 🔁
  • -[no]mol (no) — Calculate the velocity acf of molecules 🧪
  • -acflen <int> (-1) — Length of the ACF; default is half the number of frames 📏
  • -[no]normalize (yes) — Normalize the ACF ✨
  • -P <enum> (0) — Order of Legendre polynomial for the ACF (and 0 indicates none): 0, 1, 2, 3 🌀
  • -fitfn <enum> (none) — Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9 📉
  • -beginfit <real> (0) — Time where to begin the exponential fit of the correlation function 🏁
  • -endfit <real> (-1) — Time where to end the exponential fit of the correlation function; -1 means until the end 🔚

👑 SEE ALSO 👑

More info about GROMACS is available at http://www.gromacs.org/ — go read it, bestie, it's free ✨

2026, GROMACS development team

okay that's the whole page, no notes 💅 if you're still confused, that's a you problem (affectionate) — go run it and see 🫶

and that's a wrap on GMX-VELACC(1) from the GROMACS manual, version 2026.4, dated Oct 02, 2026 🎀 mwah, slay, periodt 💖✨

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