77 lines
1.7 KiB
ReStructuredText
77 lines
1.7 KiB
ReStructuredText
.. index:: dihedral_style helix
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dihedral_style helix command
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============================
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dihedral_style helix/omp command
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================================
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Syntax
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""""""
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.. code-block:: LAMMPS
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dihedral_style helix
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Examples
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""""""""
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.. code-block:: LAMMPS
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dihedral_style helix
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dihedral_coeff 1 80.0 100.0 40.0
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Description
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"""""""""""
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The *helix* dihedral style uses the potential
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.. math::
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E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
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C [1 + \cos(\theta + \frac{\pi}{4})]
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This coarse-grain dihedral potential is described in :ref:`(Guo) <Guo>`.
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For dihedral angles in the helical region, the energy function is
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represented by a standard potential consisting of three minima, one
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corresponding to the trans (t) state and the other to gauche states
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(g+ and g-). The paper describes how the :math:`A`, :math:`B` and,
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:math:`C` parameters are chosen so as to balance secondary (largely
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driven by local interactions) and
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tertiary structure (driven by long-range interactions).
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The following coefficients must be defined for each dihedral type via the
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:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
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the data file or restart files read by the :doc:`read_data <read_data>`
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or :doc:`read_restart <read_restart>` commands:
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* :math:`A` (energy)
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* :math:`B` (energy)
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* :math:`C` (energy)
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----------
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.. include:: accel_styles.rst
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----------
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Restrictions
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""""""""""""
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This dihedral style can only be used if LAMMPS was built with the
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MOLECULE package. See the :doc:`Build package <Build_package>` doc page
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for more info.
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Related commands
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""""""""""""""""
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:doc:`dihedral_coeff <dihedral_coeff>`
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**Default:** none
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----------
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.. _Guo:
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**(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
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