GMX-SANS-LEGACY(1)

✨ GMX-SANS-LEGACY(1) ✨

okay bestie, so this is a page from the GROMACS manual — manual section 1, the user commands, iykyk — and today's main character is gmx-sans-legacy. sit down, hydrate, let's get into it 💖

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🌸 NAME 🌸

gmx-sans-legacy — compute small angle neutron scattering spectra

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🦋 SYNOPSIS 🦋

gmx sans-legacy [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
             [-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]]
             [-prframe [<.xvg>]] [-sqframe [<.xvg>]] [-b <time>]
             [-e <time>] [-dt <time>] [-tu <enum>] [-xvg <enum>]
             [-mode <enum>] [-mcover <real>] [-[no]pbc]
             [-startq <real>] [-endq <real>] [-qstep <real>]
             [-seed <int>]

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💅 DESCRIPTION 💅

So gmx sans-legacy computes SANS spectra using the Debye formula. and yes, it currently uses a topology file, because it literally needs to assign an element to each atom — no elements, no vibes, no spectra. 🫶

Parameters:

• -pr — computes the normalized g(r) function, averaged over the trajectory
• -prframe — computes the normalized g(r) function for each frame
• -sq — computes the SANS intensity curve, averaged over the trajectory
• -sqframe — computes the SANS intensity curve for each frame
• -startq — starting q value, in nm
• -endq — ending q value, in nm
• -qstep — stepping in q space

Note: when you're using the Debye direct method, the computational cost goes up as 1/2 * N * (N - 1), where N is the atom number in the group of interest. it's giving quadratic, and not in a cute way. 😭

WARNING: if sq or pr are specified, this tool can produce a large number of files! up to two times larger than the number of frames! your directory is about to be booked and busy. 💀

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🎀 OPTIONS 🎀

🌈 Options to specify input files

• -s [<.tpr>] (topol.tpr) — portable xdr run input file
• -f [<.xtc/.trr/...>] (traj.xtc) — trajectory: xtc trr cpt gro g96 pdb tng h5md
• -n [<.ndx>] (index.ndx) (Optional) — index file
• -d [<.dat>] (nsfactor.dat) (Optional) — generic data file

🧚 Options to specify output files

• -pr [<.xvg>] (pr.xvg) — xvgr/xmgr file
• -sq [<.xvg>] (sq.xvg) — xvgr/xmgr file
• -prframe [<.xvg>] (prframe.xvg) (Optional) — xvgr/xmgr file
• -sqframe [<.xvg>] (sqframe.xvg) (Optional) — xvgr/xmgr file

⭐ Other options

• -b <time> (0) — time of the first frame to read from the trajectory (default unit ps)
• -e <time> (0) — time of the last frame to read from the trajectory (default unit ps)
• -dt <time> (0) — only use a frame when t MOD dt = first time (default unit ps)
• -tu <enum> (ps) — unit for time values: fs, ps, ns, us, ms, s
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -mode <enum> (direct) — mode for sans spectra calculation: direct, mc
• -mcover <real> (-1) — Monte-Carlo coverage should be -1 (default) or (0,1]
• -[no]pbc (yes) — use periodic boundary conditions for computing distances
• -startq <real> (0) — starting q (1/nm)
• -endq <real> (2) — ending q (1/nm)
• -qstep <real> (0.01) — stepping in q (1/nm)
• -seed <int> (0) — random seed for Monte-Carlo

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👑 SEE ALSO 👑

gmx(1)

more info 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, no notes 🍓✨ this was GROMACS 2026.4, dated Oct 02, 2026, straight out of the gmx-sans-legacy(1) girlies' group chat. go compute some spectra, you ate 💅🦋