---
name: "gmx-sans-legacy"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-sans-legacy"
---

# gmx-sans-legacy(1)

Compute small angle neutron scattering spectra

## NAME

gmx-sans-legacy - Compute small angle neutron scattering spectra

## 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>]
```

## DESCRIPTION

**gmx sans-legacy** computes SANS spectra using Debye formula. It currently uses topology file (since it need to assign 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

- **-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

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team