GMX-VIEW(1)

📦
version 2022.5 · 2 versions
, in debian bookworm

💅 GMX-VIEW(1) — the GROMACS manual, bestie edition 💅

okay so real talk, this is gmx-view, and it lives in section 1 of the GROMACS manual. it's the one and only gmx-view — View a trajectory on an X-Windows terminal. yes bestie, actual X Windows. she's vintage, she's iconic, we love her. 🫶

✨ NAME ✨

gmx-view — View a trajectory on an X-Windows terminal

no cap, that's literally the whole job description. she views trajectories. on an X-Windows terminal. 🎀

🌸 SYNOPSIS 🌸

gmx view [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]] [-b <time>]
         [-e <time>] [-dt <time>]

🦋 DESCRIPTION 🦋

okay so gmx view is THE GROMACS trajectory viewer. that's her whole thing, that's her main character energy. ✨

what she does: she reads a trajectory file, a run input file and an index file, and then she plots a 3D structure of your molecule right there on your standard X Window screen. periodt.

and the way she does it is SO lowkey accessible — no need for a high end graphics workstation. she even works on Monochrome screens. monochrome!! she said "your budget is not the vibe check here, we're still gonna eat." 😭💖

here's what's been implemented (the feature list, fr fr):

  • 3D view
  • rotation
  • translation and scaling of your molecule(s)
  • labels on atoms
  • animation of trajectories
  • hardcopy in PostScript format
  • user defined atom-filters
  • runs on MIT-X (real X), open windows and motif
  • user friendly menus
  • option to remove periodicity
  • option to show computational box

and because she's generous, some of the more common X command line options can be used too:

  • -bg, -fg — change colors
  • -font fontname — changes the font

slay. 💅

👑 OPTIONS 👑

💜 Options to specify input files

  • -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory: xtc trr cpt gro g96 pdb tng
  • -s [<.tpr>] (topol.tpr) — Portable xdr run input file
  • -n [<.ndx>] (index.ndx) (Optional) — Index file

🍓 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)

💀 KNOWN ISSUES 💀

not everything is flawless, bestie, and we're gonna be honest about it:

  • Balls option does not work 🙈
  • Some times dumps core without a good reason 💀
that second one is not a joke, and it's not a typo either — sometimes she just. dumps core. no reason given. no explanation. she simply chooses chaos and you must accept it. 🧚

🌈 SEE ALSO 🌈

More information about GROMACS is available at <http://www.gromacs.org/>.

go read the main page, iykyk. 📖

2023, GROMACS development team

okay that's the whole page!! 💖 this is from GROMACS version 2022.5, dated Feb 03, 2023, and yes, it's the GMX-VIEW(1) manual page. go forth and view your trajectories, you absolute icon. 🎀✨👑

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