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

# gmx-nmens(1)

Generate an ensemble of structures from the normal modes

## NAME

gmx-nmens - Generate an ensemble of structures from the normal modes

## SYNOPSIS

```
gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.gro/...>]]
          [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>]
          [-temp <real>] [-seed <int>] [-num <int>] [-first <int>]
          [-last <int>]
```

## DESCRIPTION

**gmx nmens** generates an ensemble around an average structure in a subspace that is defined by a set of normal modes (eigenvectors). The eigenvectors are assumed to be mass-weighted. The position along each eigenvector is randomly taken from a Gaussian distribution with variance kT/eigenvalue.

By default the starting eigenvector is set to 7, since the first six normal modes are the translational and rotational degrees of freedom.

## OPTIONS

Options to specify input files:

- **-v \[\<.trr/.cpt/...\>\] (eigenvec.trr)**

  Full precision trajectory: *trr* *cpt* *tng*

- **-e \[\<.xvg\>\] (eigenval.xvg)**

  xvgr/xmgr file

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

  Structure+mass(db): *tpr* *gro* *g96* *pdb* brk ent

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  Index file

Options to specify output files:

- **-o \[\<.xtc/.trr/...\>\] (ensemble.xtc)**

  Trajectory: *xtc* *trr* *gro* *g96* *pdb* *tng*

Other options:

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

- **-temp \<real\> (300)**

  Temperature in Kelvin

- **-seed \<int\> (0)**

  Random seed (0 means generate)

- **-num \<int\> (100)**

  Number of structures to generate

- **-first \<int\> (7)**

  First eigenvector to use (-1 is select)

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

  Last eigenvector to use (-1 is till the last)

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team