gmx-gyrate (1)

gmx gyrate [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]

           [-n [<.ndx>]] [-o [<.xvg>]] [-acf [<.xvg>]] [-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>] [-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.

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 and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)

    Trajectory: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)

    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Input, Optional)

    Index file

-o [<.xvg>] (gyrate.xvg) (Output)

    xvgr/xmgr file

-acf [<.xvg>] (moi-acf.xvg) (Output, Optional)

    xvgr/xmgr file

Other options:

-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

-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, vac, exp5, exp7, exp9, erffit

-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)

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