NAME

       g_rmsf - calculates atomic fluctuations

       VERSION 4.6.5

SYNOPSIS

       g_rmsf  -f  traj.xtc  -s  topol.tpr  -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od
       rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -[no]version -nice int -b time -e  time  -dt  time  -[no]w
       -xvg enum -[no]res -[no]aniso -[no]fit

DESCRIPTION

         g_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,   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

       -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

       -[no]hno
        Print help info and quit

       -[no]versionno
        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]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]resno
        Calculate averages for each residue

       -[no]anisono
        Compute anisotropic termperature factors

       -[no]fityes
        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)

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

                                                 Mon 2 Dec 2013                                        g_rmsf(1)