Provided by: gromacs-data_2019.3-2_all bug

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)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2019, GROMACS development team