Provided by: gromacs-data_4.6.5-1build1_all
g_gyrate - calculates the radius of gyration VERSION 4.6.5
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
g_gyrate computes the radius of gyration of a molecule 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.
-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
-[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 this number 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 this many 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
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_gyrate(1)