.. _gmx gyrate: gmx gyrate ========== Synopsis -------- .. parsed-literal:: gmx gyrate [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-acf` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-nmol` :emphasis:`<int>`] [:strong:`-[no]q`] [:strong:`-[no]p`] [:strong:`-[no]moi`] [:strong:`-nz` :emphasis:`<int>`] [:strong:`-acflen` :emphasis:`<int>`] [:strong:`-[no]normalize`] [:strong:`-P` :emphasis:`<enum>`] [:strong:`-fitfn` :emphasis:`<enum>`] [:strong:`-beginfit` :emphasis:`<real>`] [:strong:`-endfit` :emphasis:`<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: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng` ``-s`` [<.tpr/.gro/...>] (topol.tpr) Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`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 :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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 .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at <http://www.gromacs.org/>.