---
name: "g_saxs"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-saxs"
---

# g\_saxs(1)

Compute small angle X-ray scattering spectra

Part of [gmx-saxs(1)](/gmx-saxs/1.md).

## NAME

gmx-saxs - Compute small angle X-ray scattering spectra

## SYNOPSIS

gmx saxs \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\] \[-n \[\<.ndx\>\]\]\
          \[-d \[\<.dat\>\]\] \[-sq \[\<.xvg\>\]\] \[-nice \<int\>\] \[-b \<time\>\]\
          \[-e \<time\>\] \[-dt \<time\>\] \[-xvg \<enum\>\] \[-ng \<int\>\]\
          \[-startq \<real\>\] \[-endq \<real\>\] \[-energy \<real\>\]

## 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 and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

**-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\
     Index file

**-d** *\[\<.dat\>\] (sfactor.dat) (Input, Optional)*\
     Generic data file

**-sq** *\[\<.xvg\>\] (sq.xvg) (Output)*\
     xvgr/xmgr file

Other options:

**-nice** *\<int\> (19)*\
     Set the nicelevel

**-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 when t MOD dt = first time (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

**[gromacs(7)](/gromacs/7.md)**

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