GMX-COVAR(1)

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

✨ GMX-COVAR — it's giving "main character of your trajectory" ✨

okay so bestie, we're in the GROMACS manual pages, section 1, and today's girlie is gmx-covar 💅

🌸 NAME 🌸

gmx-covar — calculate and diagonalize the covariance matrix

🎀 SYNOPSIS 🎀

gmx covar [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
          [-o [<.xvg>]] [-v [<.trr/.cpt/...>]]
          [-av [<.gro/.g96/...>]] [-l [<.log>]] [-ascii [<.dat>]]
          [-xpm [<.xpm>]] [-xpma [<.xpm>]] [-b <time>] [-e <time>]
          [-dt <time>] [-tu <enum>] [-xvg <enum>] [-[no]fit]
          [-[no]ref] [-[no]mwa] [-last <int>] [-[no]pbc]

🦋 DESCRIPTION 🦋

so gmx covar calculates and diagonalizes the (mass-weighted) covariance matrix. that's the whole vibe. ✨

every structure gets fitted to the structure in the structure file. but — important — when that structure file is not a run input file, periodicity is not taken into account, no cap. and when the fit group and the analysis group are the same group and the analysis is non mass-weighted, then the fit is also non mass-weighted. the vibes sync up automatically, iconic.

the eigenvectors get written to a trajectory file (-v) 🎀. when the same atoms are used for both the fit and the covariance analysis, the reference structure for the fit gets written first, with t=-1. the average structure — or the reference structure when -ref is used — gets written with t=0. and then the eigenvectors get written as frames with the eigenvector number as the step number and the eigenvalue as the timestamp. cute, right?

you can then analyze those eigenvectors with gmx anaeig, bestie. go off. 🔥

option -ascii writes the whole covariance matrix to an ASCII file. the order of the elements is: x1x1, x1y1, x1z1, x1x2, ...

option -xpm writes the whole covariance matrix to an .xpm file.

option -xpma writes the atomic covariance matrix to an .xpm file — meaning for each atom pair, the sum of the xx, yy and zz covariances gets written. simple math, gorgeous execution. 💜

⚠️ okay serious moment, listen up: the diagonalization of a matrix needs memory and time that increases at least as fast as the square of the number of atoms involved. it is genuinely easy to run out of memory here, and if that happens this tool will probably exit with a 'Segmentation fault'. 😭 like, actually. you should think carefully about whether a reduced set of atoms would still meet your needs — because it's way cheaper. protect your RAM, protect your peace. 🫶

💖 OPTIONS 💖

🧚 options to specify input files

  • -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory. file types: xtc trr cpt gro g96 pdb tng h5md
  • -s [<.tpr/.gro/...>] (topol.tpr) — structure plus mass (db). file types: tpr gro g96 pdb brk ent
  • -n [<.ndx>] (index.ndx) (Optional) — the index file

🍓 options to specify output files

  • -o [<.xvg>] (eigenval.xvg) — an xvgr/xmgr file
  • -v [<.trr/.cpt/...>] (eigenvec.trr) — full precision trajectory. file types: trr cpt tng h5md
  • -av [<.gro/.g96/...>] (average.pdb) — a structure file. file types: gro g96 pdb brk ent esp
  • -l [<.log>] (covar.log) — the log file
  • -ascii [<.dat>] (covar.dat) (Optional) — a generic data file
  • -xpm [<.xpm>] (covar.xpm) (Optional) — an X PixMap compatible matrix file
  • -xpma [<.xpm>] (covara.xpm) (Optional) — an X PixMap compatible matrix 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)
  • -dt <time> (0) — only use a frame when t MOD dt = first time (default unit is ps)
  • -tu <enum> (ps) — unit for time values: fs, ps, ns, us, ms, s
  • -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
  • -[no]fit (yes) — fit to a reference structure
  • -[no]ref (no) — use the deviation from the conformation in the structure file instead of from the average
  • -[no]mwa (no) — mass-weighted covariance analysis
  • -last <int> (-1) — the last eigenvector to write away (-1 means till the last one)
  • -[no]pbc (yes) — apply corrections for periodic boundary conditions

👑 SEE ALSO 👑

gmx(1)

more info about GROMACS lives at <‐ http://www.gromacs.org/>. iykyk 🌐

2026, GROMACS development team

and that's the whole page, bestie — you ate that. 💅✨

signing off from version 2026.4, dated Oct 02, 2026 — GROMACS girlies stay winning 🫶🌸

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