GMX-GYRATE-LEGACY(1) GROMACS GMX-GYRATE-LEGACY(1) NAME gmx-gyrate-legacy - Calculate the radius of gyration SYNOPSIS 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>] DESCRIPTION gmx gyrate-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 multi- ple 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 h5md -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 in- stead 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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-GYRATE-LEGACY(1)
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