.. _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:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`]
               [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-fgroup` :emphasis:`<selection>`] [:strong:`-xvg` :emphasis:`<enum>`]
               [:strong:`-[no]rmpbc`] [:strong:`-sf` :emphasis:`<file>`] [:strong:`-selrpos` :emphasis:`<enum>`]
               [:strong:`-seltype` :emphasis:`<enum>`] [:strong:`-sel` :emphasis:`<selection>`] [:strong:`-mode` :emphasis:`<enum>`]

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 w_i (R_i(y)^2 + R_i(z)^2))/(sum_i w_i)).

where w_i is the weight value in the given situation (mass, charge, unit)

Note that this is a new implementation of the gyrate utility added in
GROMACS 2024. If you need the old one, use ``gmx gyrate-legacy``.

Options
-------

Options to specify input files:

``-f`` [<.xtc/.trr/...>] (traj.xtc) (Optional)
    Input trajectory or single configuration: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Input structure: :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Extra index groups

Options to specify output files:

``-o`` [<.xvg>] (gyrate-taf.xvg)
    Filename for gyrate plot output

Other options:

``-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 if t MOD dt == first time (ps)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-fgroup`` <selection>
    Atoms stored in the trajectory file (if not set, assume first N atoms)
``-xvg`` <enum> (xmgrace)
    Plot formatting: xmgrace, xmgr, none
``-[no]rmpbc``  (yes)
    Make molecules whole for each frame
``-sf`` <file>
    Provide selections from files
``-selrpos`` <enum> (atom)
    Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-seltype`` <enum> (atom)
    Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-sel`` <selection>
    Select group to compute gyrate radius
``-mode`` <enum> (mass)
    Atom weighting mode: mass, charge, geometry

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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