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/>.