GMX-SAXS(1)

📦
version 2023.3 · 3 versions
, in ubuntu noble

✨ GMX-SAXS(1) — the gmx-saxs page, bestie edition ✨

okay so you opened the manual for gmx-saxs, part of the GROMACS family, and honestly? iconic of you. this is the one that computes small angle X-ray scattering spectra. let's get into it 💅

🌸 NAME 🌸

gmx-saxs — Compute small angle X-ray scattering spectra

🦋 SYNOPSIS 🦋

gmx saxs [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
         [-d [<.dat>]] [-sq [<.xvg>]] [-b <time>] [-e <time>]
         [-dt <time>] [-xvg <enum>] [-ng <int>] [-startq <real>]
         [-endq <real>] [-energy <real>]

💖 DESCRIPTION 💖

so gmx saxs calculates SAXS structure factors for whatever index groups you hand it, and it does that based on Cromer's method. no cap. the catch? you need both a topology file and a trajectory file. both. it's giving "bring a friend" energy 🫶

🎀 OPTIONS 🎀

🍓 Options to specify input files:

  • -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory file, bestie. formats it vibes with: xtc trr cpt gro g96 pdb tng
  • -s [<.tpr/.gro/...>] (topol.tpr) — structure + mass(db). formats: tpr gro g96 pdb brk ent
  • -n [<.ndx>] (index.ndx) (Optional) — index file
  • -d [<.dat>] (sfactor.dat) (Optional) — generic data file

🌈 Options to specify output files:

  • -sq [<.xvg>] (sq.xvg) — xvgr/xmgr 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)
  • -xvg <enum> (xmgrace) — xvg plot formatting, and your choices are: xmgrace, xmgr, none
  • -ng <int> (1) — number of groups to compute SAXS for
  • -startq <real> (0) — starting q (1/nm)
  • -endq <real> (60) — ending q (1/nm)
  • -energy <real> (12) — energy of the incoming X-ray (keV)

🔥 SEE ALSO 🔥

more GROMACS tea is available at <http://www.gromacs.org/>. go drink it up 🧚

2023, GROMACS development team

ok that's the whole page, you ate that fr fr 💅

and that's a wrap on the GMX-SAXS(1) moment — brought to you by GROMACS version 2023.3, dated Oct 19, 2023, signed off by the GMX-SAXS(1) girlies. periodt 🎀✨

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