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<div class="section" id="dihedral-style-helix-command">
<span id="index-0"></span><h1>dihedral_style helix command</h1>
</div>
<div class="section" id="dihedral-style-helix-omp-command">
<h1>dihedral_style helix/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style helix
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>helix</em> dihedral style uses the potential</p>
<img alt="_images/dihedral_helix.jpg" class="align-center" src="_images/dihedral_helix.jpg" />
<p>This coarse-grain dihedral potential is described in <a class="reference internal" href="#guo"><span class="std std-ref">(Guo)</span></a>.
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).</p>
<p>The following coefficients must be defined for each dihedral type via the
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands:</p>
<ul class="simple">
<li>A (energy)</li>
<li>B (energy)</li>
<li>C (energy)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> 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 <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>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 <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This dihedral style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="guo"><strong>(Guo)</strong> Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).</p>
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