.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rmsf - calculates atomic fluctuations

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-q" " eiwit.pdb "
.BI "\-oq" " bfac.pdb "
.BI "\-ox" " xaver.pdb "
.BI "\-o" " rmsf.xvg "
.BI "\-od" " rmsdev.xvg "
.BI "\-oc" " correl.xvg "
.BI "\-dir" " rmsf.log "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]res" ""
.BI "\-[no]aniso" ""
.BI "\-[no]fit" ""
.SH DESCRIPTION
\&\fB g_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, \fB g_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 FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-q" " eiwit.pdb" 
.B Input, Opt.
 Protein data bank file 

.BI "\-oq" " bfac.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-ox" " xaver.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-o" " rmsf.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-od" " rmsdev.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oc" " correl.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-dir" " rmsf.log" 
.B Output, Opt.
 Log file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.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: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.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>.