.. index:: dihedral_style helix

dihedral_style helix command
============================

dihedral_style helix/omp command
================================

Syntax
""""""

.. code-block:: LAMMPS

   dihedral_style helix

Examples
""""""""

.. code-block:: LAMMPS

   dihedral_style helix
   dihedral_coeff 1 80.0 100.0 40.0

Description
"""""""""""

The *helix* dihedral style uses the potential

.. math::

   E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
       C [1 + \cos(\theta + \frac{\pi}{4})]

This coarse-grain dihedral potential is described in :ref:`(Guo) <Guo>`.
For dihedral angles in the helical region, the energy function is
represented by a standard potential consisting of three minima, one
corresponding to the trans (t) state and the other to gauche states
(g+ and g-).  The paper describes how the :math:`A`, :math:`B` and,
:math:`C` parameters are chosen so as to balance secondary (largely
driven by local interactions) and
tertiary structure (driven by long-range interactions).

The following coefficients must be defined for each dihedral type via the
:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:

* :math:`A` (energy)
* :math:`B` (energy)
* :math:`C` (energy)

----------

Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page.  The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively.  They are only enabled if
LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.

You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.

See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.

----------

Restrictions
""""""""""""

This dihedral style can only be used if LAMMPS was built with the
MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
for more info.

Related commands
""""""""""""""""

:doc:`dihedral_coeff <dihedral_coeff>`

**Default:** none

----------

.. _Guo:

**(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
