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)