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GMX-GYRATE(1) GROMACS GMX-GYRATE(1)

NAME

gmx-gyrate - Calculate the radius of gyration

SYNOPSIS

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>]


DESCRIPTION

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

Options to specify input files:

Trajectory: xtc trr cpt gro g96 pdb tng
Structure+mass(db): tpr gro g96 pdb brk ent
Index file

Options to specify output files:

xvgr/xmgr file
xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
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).
Calculate the 2D radii of gyration of this number of slices along the z-axis
Length of the ACF, default is half the number of frames
-[no]normalize (yes)
Normalize ACF
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end

SEE ALSO

gmx(1)

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COPYRIGHT

2022, GROMACS development team

June 16, 2022 2022.2