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NAME

       g_rmsf - calculates atomic fluctuations

       VERSION 4.0.1

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

DESCRIPTION

       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
       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

       -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

       -[no]xvgryes
        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -[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/>.

                                Thu 16 Oct 2008                      g_rmsf(1)