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g_nmensMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
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.
| 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 |
| 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) |