gmx-gyrate-legacy - Calculate the radius of gyration

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                              GMX-GYRATE-LEGACY(1)

gmxgyrate-legacy  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.

       gmx-gyrate-legacy - Calculate the radius of gyration

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb 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

gmx(1)

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

          gmx gyrate-legacy [-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>]