g_gyrate(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_gyrate(1)

NAME

       g_gyrate - calculates the radius of gyration

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w
       -xvg enum -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

       -[no]versionno
	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)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

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

       -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,  exp9 or  erffit

       -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 until the end

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						       g_gyrate(1)