GMX-SANS(1)

🦋 GMX-SANS — the small angle neutron scattering one (section 1, GROMACS girlie)

okay bestie so this is the manual page for gmx-sans, from the GROMACS manual, section 1. It's the tool that computes SANS spectra for you and honestly it ate. Let's get into it. 💅

---

✨ NAME ✨

gmx-sans — compute small angle neutron scattering spectra 🌸

---

✨ SYNOPSIS ✨

gmx sans [-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>]
         [-bin <real>] [-mode <enum>] [-mcover <real>]
         [-method <enum>] [-[no]pbc] [-grid <real>] [-startq <real>]
         [-endq <real>] [-qstep <real>] [-seed <int>]

---

✨ DESCRIPTION ✨

gmx sans computes SANS spectra using the Debye formula. It currently uses a topology file, because it needs to assign an element for each atom. like it literally cannot do its job without knowing what your atoms are, no cap. 🧚

Parameters, bestie:

• -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 use the Debye direct method, the computational cost increases as 1/2 * N * (N - 1), where N is the atom number in the group of interest. so it's giving quadratic. be mindful. 😭

WARNING: if sq or pr is specified, this tool can produce a large number of files! Up to two times larger than the number of frames! your directory will be absolutely full. not me finding 4000 xvg files in there 💀

---

✨ 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
• -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 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)
• -tu <enum> (ps) — unit for time values: fs, ps, ns, us, ms, s
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -bin <real> (0.2) — [HIDDEN] binwidth (nm)
• -mode <enum> (direct) — mode for sans spectra calculation: direct, mc
• -mcover <real> (-1) — Monte-Carlo coverage should be -1 (default) or (0,1]
• -method <enum> (debye) — [HIDDEN] method for sans spectra calculation: debye, fft
• -[no]pbc (yes) — use periodic boundary conditions for computing distances
• -grid <real> (0.05) — [HIDDEN] grid spacing (in nm) for FFTs
• -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

---

✨ SEE ALSO ✨

gmx(1) 🫶

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

---

✨ COPYRIGHT ✨

2023, GROMACS development team

---

okay and that's the whole page bestie!! 💖 this version dropped with GROMACS 2023.3 on Oct 19, 2023 — so if you're running it, that's the era you're living in. go compute those spectra, you're gonna slay 🌸✨🎀