gmx-gyrate man page
gmx-gyrate — Calculate the radius of gyration
gmx gyrate [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-o [<.xvg>]] [-acf [<.xvg>]] [-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>] [-beginfit <real>] [-endfit <real>]
gmx 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.
The axis components corresponds to the mass-weighted root-mean-square of the radii components orthogonal to each axis, for example:
Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).
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.
Options to specify input files:
- -f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
- -s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
- -n [<.ndx>] (index.ndx) (Optional)
Options to specify output files:
- -o [<.xvg>] (gyrate.xvg)
- -acf [<.xvg>] (moi-acf.xvg) (Optional)
- -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
- -xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
- -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).
- -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]normalize (yes)
- -P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
- -fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
- -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
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2017, GROMACS development team