Provided by: gromacs-data_4.6.5-1build1_all bug


       g_rmsf - calculates atomic fluctuations

       VERSION 4.6.5


       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


         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.


       -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


        Print help info and quit

        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)

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

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

        Calculate averages for each residue

        Compute anisotropic termperature factors

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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                g_rmsf(1)