GMX-DOS(1)

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

💖 gmx-dos 💖

okay bestie, so this is gmx-dos — straight out of the GROMACS manual, and it's the one that reads the density of states out of your simulation and then tells you stuff based on it. it's giving "vibrational spectroscopy but make it a command line tool". slay. 🎀

✨ NAME ✨

gmx-dos — analyze density of states and properties based on that 🦋

🌸 SYNOPSIS 🌸

gmx dos [-f [<.trr/.cpt/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
        [-vacf [<.xvg>]] [-mvacf [<.xvg>]] [-dos [<.xvg>]]
        [-g [<.log>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
        [-xvg <enum>] [-[no]v] [-[no]recip] [-[no]abs] [-[no]normdos]
        [-T <real>] [-acflen <int>] [-[no]normalize] [-P <enum>]
        [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]

💅 DESCRIPTION 💅

So gmx dos computes the Density of States from a simulation. periodt. 💫

but like… for this to actually mean anything, the velocities have to be saved in the trajecotry with a sufficiently high frequency so that you cover all the vibrations. for flexible systems that's around a few fs between saving. no cap, if you skimp on the saving frequency you're just vibing with noise. 😭

Properties based on the DoS get printed on the standard output. 🖨️

and now the important part, bestie — lowkey read this twice: the density of states is calculated from the mass-weighted autocorrelation, and by default only from the square of the real component rather than the absolute value. what does that mean for you? it means the shape can differ substantially from the plain vibrational power spectrum you'd get with gmx velacc. so if your DoS looks different from your power spectrum, that's not a bug, that's the vibe. 🫶

✨ OPTIONS ✨

🎀 Options to specify input files

  • -f [<.trr/.cpt/...>] (traj.trr) — full precision trajectory. can take trr cpt tng h5md. the whole cinematic universe of trajectory formats basically 💖
  • -s [<.tpr>] (topol.tpr) — portable xdr run input file. your little structural blueprint 🧚
  • -n [<.ndx>] (index.ndx) (Optional) — index file. optional, so only if you want it 🍓

🌈 Options to specify output files

  • -vacf [<.xvg>] (vacf.xvg) — xvgr/xmgr file
  • -mvacf [<.xvg>] (mvacf.xvg) — xvgr/xmgr file
  • -dos [<.xvg>] (dos.xvg) — xvgr/xmgr file
  • -g [<.log>] (dos.log) — log file. receipts, kept ✍️

👑 Other options

  • -b <time> (0) — time of first frame to read from trajectory (default unit ps)
  • -e <time> (0) — time of last frame to read from trajectory (default unit ps)
  • -dt <time> (0) — only use frame when t MOD dt = first time (default unit ps)
  • -[no]w (no) — view output .xvg, .xpm, .eps and .pdb files. the whole "ooh pretty plots" button 👀
  • -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
  • -[no]v (yes) — be loud and noisy. and honestly? default is on because we love a chatty program 💬
  • -[no]recip (no) — use cm^-1 on X-axis instead of 1/ps for DoS plots. wavenumber girlies rise 🙌
  • -[no]abs (no) — use the absolute value of the Fourier transform of the VACF as the Density of States. default is to use the real component only
  • -[no]normdos (no) — normalize the DoS such that it adds up to 3N. this should usually not be necessary. like fr, usually don't 💀
  • -T <real> (298.15) — temperature in the simulation. room temp coded in by default, cute 🌡️
  • -acflen <int> (-1) — length of the ACF, default is half the number of frames
  • -[no]normalize (yes) — normalize ACF
  • -P <enum> (0) — order of Legendre polynomial for ACF (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 is until the end

⚠️ KNOWN ISSUES ⚠️

  • This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision). 💀 bestie this will eat your RAM for breakfast. plan accordingly. 🍽️

🦋 SEE ALSO 🦋

2026, GROMACS development team — they made it, we just gossip about it 🫶

and that's the whole page, bestie!! go analyze those density of states, you absolute icon 👑

this has been gmx-dos for GROMACS, version 2026.4, dated Oct 02, 2026. mwah, take care of your trajectory save frequency 💖✨🎀

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