forked from lijiext/lammps
104 lines
2.8 KiB
Plaintext
104 lines
2.8 KiB
Plaintext
.. 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 *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 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
|