g_gyrate VERSION 3.3_beta_20050823

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 -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

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.

-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb xml

-n index.ndx Input, Opt. Index file

-o gyrate.xvg Output xvgr/xmgr file

-acf moi-acf.xvg Output, Opt. xvgr/xmgr file

-[no]h no 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]w no View output xvg, xpm, eps and pdb files

-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-nmol int 1 The number of molecules to analyze

-[no]q no Use absolute value of the charge of an atom as weighting factor instead of mass

-[no]p no Calculate the radii of gyration about the principal axes.

-[no]moi no Calculate the moments of inertia (defined by the principal axes).

-acflen int -1 Length of the ACF, default is half the number of frames

-[no]normalize yes 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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.