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       g_rmsf - calculates atomic fluctuations

       VERSION 4.0.1


       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  -nice  int  -b  time -e time -dt time -[no]w -[no]xvgr -[no]res
       -[no]aniso -[no]fit


       g_rmsf computes the root mean square fluctuation (RMSF,  i.e.  standard
       deviation)   of  atomic  positions  after  (optionally)  fitting  to  a
       reference frame.

       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


       -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

       -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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

        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



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                      g_rmsf(1)