---
name: "g_rmsf_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-rmsf"
---

# g\_rmsf\_d(1)

Calculate atomic fluctuations

Part of [gmx-rmsf(1)](/gmx-rmsf/1.md).

## NAME

gmx-rmsf - Calculate atomic fluctuations

## SYNOPSIS

gmx rmsf \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\] \[-n \[\<.ndx\>\]\]\
          \[-q \[\<.pdb\>\]\] \[-oq \[\<.pdb\>\]\] \[-ox \[\<.pdb\>\]\] \[-o \[\<.xvg\>\]\]\
          \[-od \[\<.xvg\>\]\] \[-oc \[\<.xvg\>\]\] \[-dir \[\<.log\>\]\] \[-nice \<int\>\]\
          \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\] \[-\[no\]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 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**, **gmx 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.

## OPTIONS

Options to specify input and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

**-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\
     Index file

**-q** *\[\<.pdb\>\] (eiwit.pdb) (Input, Optional)*\
     Protein data bank file

**-oq** *\[\<.pdb\>\] (bfac.pdb) (Output, Optional)*\
     Protein data bank file

**-ox** *\[\<.pdb\>\] (xaver.pdb) (Output, Optional)*\
     Protein data bank file

**-o** *\[\<.xvg\>\] (rmsf.xvg) (Output)*\
     xvgr/xmgr file

**-od** *\[\<.xvg\>\] (rmsdev.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-oc** *\[\<.xvg\>\] (correl.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-dir** *\[\<.log\>\] (rmsf.log) (Output, Optional)*\
     Log file

Other options:

**-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**  *(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 termperature 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

**[gromacs(7)](/gromacs/7.md)**

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