Man Linux: Main Page and Category List


       g_gyrate - calculates the radius of gyration

       VERSION 4.0.1


       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


       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

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


       -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


        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

       -nmol int 1
        The number of molecules to analyze

        Use absolute value of the  charge  of  an  atom  as  weighting  factor
       instead of mass

        Calculate the radii of gyration about the principal axes.

        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

        Normalize ACF

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

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

       -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



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                    g_gyrate(1)