---
name: "gmx-rmsf"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-rmsf"
---

# gmx-rmsf(1)

Calculate atomic fluctuations

## NAME

gmx-rmsf - Calculate atomic fluctuations

## SYNOPSIS

```
gmx rmsf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
         [-q [<.pdb>]] [-oq [<.pdb>]] [-ox [<.pdb>]] [-o [<.xvg>]]
         [-od [<.xvg>]] [-oc [<.xvg>]] [-dir [<.log>]] [-b <time>]
         [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]res]
         [-[no]aniso] [-[no]fit]
```

## DESCRIPTION

**gmx rmsf** computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with **-f**) after (optionally) fitting to a reference frame (supplied with **-s**).

With option **-oq** the RMSF values are converted to B-factor values, which are written to a *.pdb* file. By default, the coordinates in this output file are taken from the structure file provided with **-s**,although you can also use coordinates read from a different *.pdb* fileprovided with **-q**. There is very little error checking, so in this caseit is your responsibility to make sure all atoms in the structure fileand *.pdb* file correspond exactly to each other.

Option **-ox** writes the B-factors to a file with the average coordinates in the trajectory.

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

With the option **-aniso**, **gmx rmsf** will compute anisotropic temperature factors and then it will also output average coordinates and a *.pdb* file with ANISOU records (corresponding 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.

## OPTIONS

Options to specify input files:

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc)**

  Trajectory: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

- **-s \[\<.tpr/.gro/...\>\] (topol.tpr)**

  Structure+mass(db): *tpr* *gro* *g96* *pdb* brk ent

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  Index file

- **-q \[\<.pdb\>\] (eiwit.pdb) (Optional)**

  Protein data bank file

Options to specify output files:

- **-oq \[\<.pdb\>\] (bfac.pdb) (Optional)**

  Protein data bank file

- **-ox \[\<.pdb\>\] (xaver.pdb) (Optional)**

  Protein data bank file

- **-o \[\<.xvg\>\] (rmsf.xvg)**

  xvgr/xmgr file

- **-od \[\<.xvg\>\] (rmsdev.xvg) (Optional)**

  xvgr/xmgr file

- **-oc \[\<.xvg\>\] (correl.xvg) (Optional)**

  xvgr/xmgr file

- **-dir \[\<.log\>\] (rmsf.log) (Optional)**

  Log file

Other options:

- **-b \<time\> (0)**

  Time of first frame to read from trajectory (default unit ps)

- **-e \<time\> (0)**

  Time of last frame to read from trajectory (default unit ps)

- **-dt \<time\> (0)**

  Only use frame when t MOD dt = first time (default unit ps)

- **-\[no\]w (no)**

  View output *.xvg*, *.xpm*, *.eps* and *.pdb* files

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

- **-\[no\]res (no)**

  Calculate averages for each residue

- **-\[no\]aniso (no)**

  Compute anisotropic temperature factors

- **-\[no\]fit (yes)**

  Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team