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g_covarMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
g_covar calculates and diagonalizes the (mass-weighted) covariance matrix. All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. When the fit and analysis groups are identical and the analysis is non mass-weighted, the fit will also be non mass-weighted.
The eigenvectors are written to a trajectory file (-v). When the same atoms are used for the fit and the covariance analysis, the reference structure for the fit is written first with t=-1. The average (or reference when -ref is used) structure is written with t=0, the eigenvectors are written as frames with the eigenvector number as timestamp.
The eigenvectors can be analyzed with g_anaeig.
Option -ascii writes the whole covariance matrix to an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
Option -xpm writes the whole covariance matrix to an xpm file.
Option -xpma writes the atomic covariance matrix to an xpm file, i.e. for each atom pair the sum of the xx, yy and zz covariances is written.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Trajectory: xtc trr trj gro g96 pdb cpt |
| -s | topol.tpr | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -n | index.ndx | Input, Opt. | Index file |
| -o | eigenval.xvg | Output | xvgr/xmgr file |
| -v | eigenvec.trr | Output | Full precision trajectory: trr trj cpt |
| -av | average.pdb | Output | Structure file: gro g96 pdb etc. |
| -l | covar.log | Output | Log file |
| -ascii | covar.dat | Output, Opt. | Generic data file |
| -xpm | covar.xpm | Output, Opt. | X PixMap compatible matrix file |
| -xpma | covara.xpm | Output, Opt. | X PixMap compatible matrix file |
| 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 |
| -b | time | 0 | First frame (ps) to read from trajectory |
| -e | time | 0 | Last frame (ps) to read from trajectory |
| -dt | time | 0 | Only use frame when t MOD dt = first time (ps) |
| -tu | enum | ps | Time unit: fs, ps, ns, us, ms or s |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -[no]fit | gmx_bool | yes | Fit to a reference structure |
| -[no]ref | gmx_bool | no | Use the deviation from the conformation in the structure file instead of from the average |
| -[no]mwa | gmx_bool | no | Mass-weighted covariance analysis |
| -last | int | -1 | Last eigenvector to write away (-1 is till the last) |
| -[no]pbc | gmx_bool | yes | Apply corrections for periodic boundary conditions |