g_rmsf

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

### Description

g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame.

With option `-oq` the RMSF values are converted to B-factor values, which are written to a pdb file with the coordinates, of the structure file, or of a pdb file when `-q` is specified. Option `-ox` writes the B-factors to a file with the average coordinates.

With the option `-od` the root mean square deviation with respect to the reference structure is calculated.

With the option `aniso` g_rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a pdb file with ANISOU records (corresonding to the `-oq` or `-ox` option). Please note that the U values are orientation dependent, so before comparison with experimental data you should verify that you fit to the experimental coordinates.

When a pdb input file is passed to the program and the `-aniso` flag is set a correlation plot of the Uij will be created, if any anisotropic temperature factors are present in the pdb file.

With option `-dir` the average MSF (3x3) matrix is diagonalized. This shows the directions in which the atoms fluctuate the most and the least.

### 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
`-q` | `eiwit.pdb` | Input, Opt. | Protein data bank file
`-oq` | `bfac.pdb` | Output, Opt. | Protein data bank file
`-ox` | `xaver.pdb` | Output, Opt. | Protein data bank file
`-o` | `rmsf.xvg` | Output | xvgr/xmgr file
`-od` | `rmsdev.xvg` | Output, Opt. | xvgr/xmgr file
`-oc` | `correl.xvg` | Output, Opt. | xvgr/xmgr file
`-dir` | `rmsf.log` | Output, Opt. | Log 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)
`-[no]w` | gmx_bool | `no` | View output xvg, xpm, eps and pdb files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-[no]res` | gmx_bool | `no` | Calculate averages for each residue
`-[no]aniso` | gmx_bool | `no` | Compute anisotropic termperature factors
`-[no]fit` | gmx_bool | `yes` | Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.

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