.. 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) `. 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 ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`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 ` 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 ` 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 ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. See :doc:`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 ` section for more info on packages. Related commands """""""""""""""" :doc:`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