## g_nmens

Main Table of Contents

VERSION 4.5
Thu 26 Aug 2010

### Description

`g_nmens` generates an ensemble around an average structure in a subspace which 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.

### Files

option | filename | type | description
--- | --- | --- | ---
`-v` | `eigenvec.trr` | Input | Full precision trajectory: trr trj cpt
`-e` | `eigenval.xvg` | Input | xvgr/xmgr file
`-s` | `topol.tpr` | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-n` | `index.ndx` | Input, Opt. | Index file
`-o` | `ensemble.xtc` | Output | Trajectory: xtc trr trj gro g96 pdb

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | gmx_bool | `no` | Print help info and quit
`-[no]version` | gmx_bool | `no` | Print version info and quit
`-nice` | int | `19` | Set the nicelevel
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `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)

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