| ## g_covar Main Table of Contents | VERSION 4.5 Thu 26 Aug 2010

### Description

`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.

### Files

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

### 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
`-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

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