---
name: "gmx-sans"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2022.5-2"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-sans"
---

# gmx-sans(1)

Compute small angle neutron scattering spectra

## 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 Debye formula.* *It currently uses topology file (since it need to assigne element for each atom).*

*Parameters:*

**-pr** *Computes normalized g(r) function averaged over trajectory*

**-prframe** *Computes normalized g(r) function for each frame*

**-sq** *Computes SANS intensity curve averaged over trajectory*

**-sqframe** *Computes 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 using Debye direct method computational cost increases as* *1/2 \* N \* (N - 1) where N is atom number in group of interest.*

*WARNING: If sq or pr specified this tool can produce large number of files! Up to* *two times larger than number of frames!*

## 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)](/gmx/1.md)**

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

## COPYRIGHT

*2023, GROMACS development team*