g_gyrate(1)

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/>.