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g_nmeigMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated with mdrun. The eigenvectors are written to a trajectory file (-v). The structure is written first with t=0. The eigenvectors are written as frames with the eigenvector number as timestamp. The eigenvectors can be analyzed with g_anaeig. An ensemble of structures can be generated from the eigenvectors with g_nmens. When mass weighting is used, the generated eigenvectors will be scaled back to plain cartesian coordinates before generating the output - in this case they will no longer be exactly orthogonal in the standard cartesian norm (But in the mass weighted norm they would be).
| option | filename | type | description |
|---|---|---|---|
| -f | hessian.mtx | Input | Hessian matrix |
| -s | topol.tpr | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -of | eigenfreq.xvg | Output | xvgr/xmgr file |
| -ol | eigenval.xvg | Output | xvgr/xmgr file |
| -v | eigenvec.trr | Output | Full precision trajectory: trr trj cpt |
| 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 |
| -[no]m | gmx_bool | yes | Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis |
| -first | int | 1 | First eigenvector to write away |
| -last | int | 50 | Last eigenvector to write away |