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

# gmx-saxs(1)

Compute small angle X-ray scattering spectra

## 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

**gmx saxs** *calculates SAXS structure factors for given index* *groups based on Cromer's method.* *Both topology and trajectory files are required.*

## OPTIONS

*Options to specify input files:*

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc)**

  *Trajectory: xtc trr cpt gro g96 pdb tng*

- **-s \[\<.tpr/.gro/...\>\] (topol.tpr)**

  *Structure+mass(db): 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: xmgrace, xmgr, none*

- **-ng \<int\> (1)**

  *Number of groups to compute SAXS*

- **-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

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

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

## COPYRIGHT

*2023, GROMACS development team*