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

# g\_nmens(1)

Generate an ensemble of structures from the normal modes

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

## NAME

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

## SYNOPSIS

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

## 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 and output files:

**-v** *\[\<.trr/.cpt/...\>\] (eigenvec.trr) (Input)*\
     Full precision trajectory: trr cpt trj tng

**-e** *\[\<.xvg\>\] (eigenval.xvg) (Input)*\
     xvgr/xmgr file

**-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

**-o** *\[\<.xtc/.trr/...\>\] (ensemble.xtc) (Output)*\
     Trajectory: xtc trr trj gro g96 pdb tng

Other options:

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

**-xvg** *\<enum\> (xmgrace)*\
     xvg plot formatting: xmgrace, xmgr, none

**-temp** *\<real\> (300)*\
     Temperature in Kelvin

**-seed** *\<int\> (-1)*\
     Random seed, -1 generates a seed from time and pid

**-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

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

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