.TH gmx-rmsf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-rmsf \- Calculate atomic fluctuations

.SH 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]

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

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

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

With the option \fB\-aniso\fR, \fBgmx rmsf\fR will compute anisotropic temperature factors and then it will also output average coordinates and a \fB.pdb\fR file with ANISOU records (corresonding to the \fB\-oq\fR or \fB\-ox\fR 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 \fB.pdb\fR input file is passed to the program and the \fB\-aniso\fR flag is set a correlation plot of the Uij will be created, if any anisotropic temperature factors are present in the \fB.pdb\fR file.

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

.SH OPTIONS
Options to specify input and output files:

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

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

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

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

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

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

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

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

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

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


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-[no]res" "  (no)"
    Calculate averages for each residue

.BI "\-[no]aniso" "  (no)"
    Compute anisotropic termperature factors

.BI "\-[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.


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.