.. _gmx helix:

gmx helix
=========

Synopsis
--------

.. parsed-literal::

    gmx helix [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`]
              [:strong:`-cz` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
              [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-r0` :emphasis:`<int>`] [:strong:`-[no]q`] [:strong:`-[no]F`]
              [:strong:`-[no]db`] [:strong:`-[no]ev`] [:strong:`-ahxstart` :emphasis:`<int>`] [:strong:`-ahxend` :emphasis:`<int>`]

Description
-----------

``gmx helix`` computes all kinds of helix properties. First, the peptide
is checked to find the longest helical part, as determined by
hydrogen bonds and phi/psi angles.
That bit is fitted
to an ideal helix around the *z*-axis and centered around the origin.
Then the following properties are computed:

 * Helix radius (file ``radius.xvg``). This is merely the
   RMS deviation in two dimensions for all Calpha atoms.
   it is calculated as sqrt((sum_i (x^2(i)+y^2(i)))/N) where N is
   the number of backbone atoms. For an ideal helix the radius is 0.23 nm.
 * Twist (file ``twist.xvg``). The average helical angle per
   residue is calculated. For an alpha-helix it is 100 degrees,
   for 3-10 helices it will be smaller, and
   for 5-helices it will be larger.
 * Rise per residue (file ``rise.xvg``). The helical rise per
   residue is plotted as the difference in *z*-coordinate between Calpha
   atoms. For an ideal helix, this is 0.15 nm.
 * Total helix length (file ``len-ahx.xvg``). The total length
   of the
   helix in nm. This is simply the average rise (see above) times the
   number of helical residues (see below).
 * Helix dipole, backbone only (file ``dip-ahx.xvg``).
 * RMS deviation from ideal helix, calculated for the Calpha
   atoms only (file ``rms-ahx.xvg``).
 * Average Calpha - Calpha dihedral angle (file ``phi-ahx.xvg``).
 * Average phi and psi angles (file ``phipsi.xvg``).
 * Ellipticity at 222 nm according to Hirst and Brooks.

Options
-------

Options to specify input files:

``-s`` [<.tpr>] (topol.tpr)
    Portable xdr run input file
``-n`` [<.ndx>] (index.ndx)
    Index file
``-f`` [<.xtc/.trr/...>] (traj.xtc)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`

Options to specify output files:

``-cz`` [<.gro/.g96/...>] (zconf.gro)
    Structure file: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp

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
``-r0`` <int> (1)
    The first residue number in the sequence
``-[no]q``  (no)
    Check at every step which part of the sequence is helical
``-[no]F``  (yes)
    Toggle fit to a perfect helix
``-[no]db``  (no)
    Print debug info
``-[no]ev``  (no)
    Write a new 'trajectory' file for ED
``-ahxstart`` <int> (0)
    First residue in helix
``-ahxend`` <int> (0)
    Last residue in helix

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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