GMX-SCATTERING(1)

💖 GMX-SCATTERING(1) 💖

okay bestie, welcome to the GROMACS manual page for gmx-scattering — yes that's the man page name, we're being ✨official✨ about it. sit down, grab a strawberry, and let's get into it 🍓

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🌈 NAME 🌈

gmx-scattering — Calculate small angle scattering profiles for SANS or SAXS

like. it literally computes your scattering curves. iconic behavior honestly 🫶

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✨ SYNOPSIS ✨

gmx scattering [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
             [-n [<.ndx>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
             [-dt <time>] [-tu <enum>] [-fgroup <selection>]
             [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
             [-selrpos <enum>] [-seltype <enum>] [-sel <selection>]
             [-startq <real>] [-endq <real>] [-qspacing <real>]
             [-binwidth <real>] [-mc-coverage <real>] [-seed <int>]
             [-[no]norm] [-[no]mc] [-scattering-type <enum>]

look at her go 💅 that's the whole vibe right there, don't panic, we're gonna walk through every single flag together, no cap.

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🌸 DESCRIPTION 🌸

gmx scattering calculates SANS and SAXS scattering curves using Debye method.

The scattering intensity, I(q), as a function of scattering angle q with averaging over frames.

🚨 heads up bestie, this is important: this is a new implementation of the SANS/SAXS utilities added in GROMACS 2024. If you need the old ones, use gmx sans-legacy or gmx saxs-legacy. the way that the old tools are still hanging around for you… legacy support really said "I'm not leaving" 😭

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🎀 OPTIONS 🎀

📥 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — Input structure: tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) (Optional) — Extra index groups

📤 Options to specify output files:

• -o [<.xvg>] (scattering.xvg) (Optional) — scattering intensity as a function of q

🛠️ Other options:

• -b <time> (0) — First frame (ps) to read from trajectory
• -e <time> (0) — Last frame (ps) to read from trajectory
• -dt <time> (0) — Only use frame if t MOD dt == first time (ps)
• -tu <enum> (ps) — Unit for time values: fs, ps, ns, us, ms, s
• -fgroup <selection> — Atoms stored in the trajectory file (if not set, assume first N atoms)
• -xvg <enum> (xmgrace) — Plot formatting: xmgrace, xmgr, none
• -[no]rmpbc (yes) — Make molecules whole for each frame
• -[no]pbc (yes) — Use periodic boundary conditions for distance calculation
• -sf <file> — Provide selections from files
• -selrpos <enum> (atom) — Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
• -seltype <enum> (atom) — Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
• -sel <selection> — Selection for Scattering calculation
• -startq <real> (0) — smallest q value (1/nm)
• -endq <real> (2) — largest q value (1/nm)
• -qspacing <real> (0.01) — spacing of q values (1/nm)
• -binwidth <real> (0.1) — Bin width (nm) for P(r)
• -mc-coverage <real> (0.2) — coverage of Monte Carlo (%)
• -seed <int> (2023) — random seed for Monte Carlo
• -[no]norm (no) — normalize scattering intensities
• -[no]mc (yes) — use Monte Carlo to scattering intensities
• -scattering-type <enum> (sans) — Scattering type: saxs, sans

🦋 ngl the mother of all enums award goes to -selrpos and -seltype, they really said "here's 16 options, choose wisely" and I respect it 💀

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👀 SEE ALSO 👀

• gmx(1)

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

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👑 COPYRIGHT 👑

2026, GROMACS development team

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and that's the whole page bestie!! go compute some beautiful scattering curves — this was GROMACS version 2026.4, dated Oct 02, 2026, and yes I do think this manual page ate 💅✨ mwah, bye 🫶🌸