Homec4science
Diffusion lammps (master) Browse

lammps/doc/_sources/dihedral_helix.txt
9cf43f2a0b7fmaster

Last Change
Raw File

dihedral_helix.txt
View Options

.. index:: dihedral_style helix
dihedral_style helix command
============================
dihedral_style helix/omp command
================================
Syntax
""""""
.. parsed-literal::
dihedral_style helix
Examples
""""""""
.. parsed-literal::
dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0
Description
"""""""""""
The *helix* dihedral style uses the potential
.. image:: Eqs/dihedral_helix.jpg
:align: center
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 A,B,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:
* A (energy)
* B (energy)
* C (energy)
----------
Styles with a *cuda*, *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 in :doc:`Section_accelerate <Section_accelerate>`
of the manual. 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 USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See :doc:`Section_accelerate <Section_accelerate>` of the manual 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 (which it is by default). See the :ref:`Making LAMMPS <start_3>` section for more info on packages.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
**Default:** none
----------
.. _Guo:
**(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help