GMX-POLYSTAT(1)

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

💖 GMX-POLYSTAT(1) 💖

okay bestie, welcome to gmx-polystat</c> — it's the GROMACS tool that does static polymer properties, and yes it's literally as iconic as it sounds. calculating the static properties of polymers?? we love to see it. 🧚✨

🌸 NAME 🌸

gmx-polystat — Calculate static properties of polymers 💅

No wait, that's the whole point. Sit down, grab a boba, let's go. 🍓

✨ SYNOPSIS ✨

gmx polystat [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
             [-o [<.xvg>]] [-v [<.xvg>]] [-p [<.xvg>]] [-i [<.xvg>]]
             [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
             [-[no]w] [-xvg <enum>] [-[no]mw] [-[no]pc]

that's the whole vibe right there. every flag is a little lewk. 👑

🦋 DESCRIPTION 🦋

so gmx polystat plots static properties of polymers as a function of time, and then it prints the average. plotting AND averaging?? multitasking queen. 💅

by default it figures out the average end-to-end distance and the radii of gyration of your polymers. it asks you for an index group and then splits that group into molecules. then, for each molecule, the end-to-end distance gets determined using the first and the last atom in the index group. no cap, that's just how it works. ✨

for the radius of gyration, it writes the total and the three principal components for the average gyration tensor. so you get the full set, not just a teaser.

  • with option -v the eigenvectors get written. icon behaviour. 🎀
  • with option -pc the average eigenvalues of the individual gyration tensors get written too.
  • with option -i the mean square internal distances get written.

🌈 the persistence length arc 🌈

with option -p the persistence length gets determined. heads up bestie: the index group you pick should consist of atoms that are consecutively bonded in the polymer mainchains. like, that's non-negotiable, it's giving structural prerequisite. 🌸

the persistence length is then determined from the cosine of the angles between bonds with an index difference that is even. the odd pairs do not get used — and here's the why: straight polymer backbones are usually all trans, and therefore only every second bond aligns. so the odd ones are just out here not aligning. not their fault, but we skip them. 💀

the persistence length is defined as the number of bonds where the average cos reaches a value of 1/e. that point is determined by a linear interpolation of log(<cos>). math ate, fr fr. 🔥

👑 OPTIONS 👑

🎀 options to specify input files 🎀

  • -s [<.tpr>] (topol.tpr) — Portable xdr run input file. the little blueprint of your sim, love that for us.
  • -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory: xtc trr cpt gro g96 pdb tng h5md. so many formats, so little time, we literally accept all of them. 🦋
  • -n [<.ndx>] (index.ndx) (Optional) — Index file. optional but honestly the moment you need groups you'll want it. 🙈

🍓 options to specify output files 🍓

  • -o [<.xvg>] (polystat.xvg) — xvgr/xmgr file. the main character output. ✨
  • -v [<.xvg>] (polyvec.xvg) (Optional) — xvgr/xmgr file. the eigenvectors girlies.
  • -p [<.xvg>] (persist.xvg) (Optional) — xvgr/xmgr file. persistence length data, served fresh.
  • -i [<.xvg>] (intdist.xvg) (Optional) — xvgr/xmgr file. internal distances, so demure.

💅 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). yes the modular arithmetic is doing its thing, trust. 😭
  • -tu <enum> (ps) — Unit for time values: fs, ps, ns, us, ms, s. pick your time era bestie. ⭐
  • -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files. turn it on and it literally opens them up for your viewing pleasure. 👀
  • -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none. choose your plot aesthetic. 🎀
  • -[no]mw (yes) — Use the mass weighting for radii of gyration. it's on by default and lowkey that's the right call.
  • -[no]pc (no) — Plot average eigenvalues. off by default, flip it on and the eigenvalues get their moment. 💜

🌈 SEE ALSO 🌈

More information about GROMACS is available at <http://www.gromacs.org/>. go forth and read, it's giving lore. 📚✨

2026, GROMACS development team

and that's the whole page bestie!! 🫶 no cap, you're now fully qualified to police polymer statistics. this was GROMACS 2026.4, dated Oct 02, 2026, and honestly? iconic of them. slay, periodt. 💅✨😭

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