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NAME

       g_gyrate - calculates the radius of gyration

       VERSION 4.0.1

SYNOPSIS

       g_gyrate  -f  traj.xtc  -s  topol.tpr  -n  index.ndx -o gyrate.xvg -acf
       moi-acf.xvg -[no]h -nice int -b time -e time -dt time -[no]w  -[no]xvgr
       -nmol  int -[no]q -[no]p -[no]moi -nz int -acflen int -[no]normalize -P
       enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION

       g_gyrate computes the radius of gyration of a group of  atoms  and  the
       radii of gyration about the x, y and z axes, as a function of time. The
       atoms are explicitly mass weighted.

       With the  -nmol option the radius of gyration will  be  calculated  for
       multiple  molecules  by  splitting  the analysis group in equally sized
       parts.

       With the option  -nz 2D radii of gyration in the x-y  plane  of  slices
       along the z-axis are calculated.

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

       -o gyrate.xvg Output
        xvgr/xmgr file

       -acf moi-acf.xvg Output, Opt.
        xvgr/xmgr 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

       -nmol int 1
        The number of molecules to analyze

       -[no]qno
        Use absolute value of the  charge  of  an  atom  as  weighting  factor
       instead of mass

       -[no]pno
        Calculate the radii of gyration about the principal axes.

       -[no]moino
        Calculate the moments of inertia (defined by the principal axes).

       -nz int 0
        Calculate the 2D radii of gyration of  slices along the z-axis

       -acflen int -1
        Length of the ACF, default is half the number of frames

       -[no]normalizeyes
        Normalize ACF

       -P enum 0
        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or
       3

       -fitfn enum none
        Fit function:  none,  exp,  aexp,   exp_exp,   vac,   exp5,   exp7  or
       exp9

       -ncskip int 0
        Skip N points in the output file of correlation functions

       -beginfit real 0
        Time where to begin the exponential fit of the correlation function

       -endfit real -1
        Time  where to end the exponential fit of the correlation function, -1
       is till the end

SEE ALSO

       gromacs(7)

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

                                Thu 16 Oct 2008                    g_gyrate(1)