g_gyrate (1) Linux Manual Page

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/>.