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:

-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)
    Index file

    Options to specify output files:

-o [<.xvg>] (gyrate.xvg)
    xvgr/xmgr file

-acf [<.xvg>] (moi-acf.xvg) (Optional)
    xvgr/xmgr file

    Other options:

-b <time> (0)
    Time of first frame to read from trajectory (default unit ps)

-e <time> (0)
    Time of last frame to read from trajectory (default unit ps)

-dt <time> (0)
    Only use frame when t MOD dt = first time (default unit 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)
    Normalize ACF

-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

SEE ALSO

gmx(1)

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