Page MenuHomec4science
Files F97302600

dihedral_style.html
No OneTemporary
Actions

File Metadata

Created
Sat, Jan 4, 04:34

dihedral_style.html
View Options

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>dihedral_style command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>dihedral_style command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="dihedral-style-command">
<span id="index-0"></span><h1>dihedral_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style style
</pre>
<ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or <em>multi/harmonic</em> or <em>opls</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
<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> command
from a data or restart file.</p>
<p>Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the <em>hybrid</em> dihedral style.</p>
<p>The coefficients associated with a dihedral style can be specified in
a data or restart file or via the <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>
command.</p>
<p>All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> commands do not need to be
re-specified in an input script that restarts a simulation. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for details on how to do
this. The one exception is that dihedral_style <em>hybrid</em> only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When both a dihedral and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.</p>
</div>
<p>In the formulas listed for each dihedral style, <em>phi</em> is the torsional
angle defined by the quadruplet of atoms. This angle has a sign
convention as shown in this diagram:</p>
<img alt="_images/dihedral_sign.jpg" class="align-center" src="_images/dihedral_sign.jpg" />
<p>where the I,J,K,L ordering of the 4 atoms that define the dihedral
is from left to right.</p>
<p>This sign convention effects several of the dihedral styles listed
below (e.g. charmm, helix) in the sense that the energy formula
depends on the sign of phi, which may be reflected in the value of the
coefficients you specify.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When comparing the formulas and coefficients for various LAMMPS
dihedral styles with dihedral equations defined by other force fields,
note that some force field implementations divide/multiply the energy
prefactor <em>K</em> by the multiple number of torsions that contain the J-K
bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
dihedral equation applies to each individual dihedral. Thus you need
to define <em>K</em> appropriately via the
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command to account for this
difference if necessary.</p>
</div>
<hr class="docutils" />
<p>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command.</p>
<p>Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the dihedral section of
<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="dihedral_none.html"><span class="doc">dihedral_style none</span></a> - turn off dihedral interactions</li>
<li><a class="reference internal" href="dihedral_zero.html"><span class="doc">dihedral_style zero</span></a> - topology but no interactions</li>
<li><a class="reference internal" href="dihedral_hybrid.html"><span class="doc">dihedral_style hybrid</span></a> - define multiple styles of dihedral interactions</li>
<li><a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style charmm</span></a> - CHARMM dihedral</li>
<li><a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a> - COMPASS (class 2) dihedral</li>
<li><a class="reference internal" href="dihedral_harmonic.html"><span class="doc">dihedral_style harmonic</span></a> - harmonic dihedral</li>
<li><a class="reference internal" href="dihedral_helix.html"><span class="doc">dihedral_style helix</span></a> - helix dihedral</li>
<li><a class="reference internal" href="dihedral_multi_harmonic.html"><span class="doc">dihedral_style multi/harmonic</span></a> - multi-harmonic dihedral</li>
<li><a class="reference internal" href="dihedral_opls.html"><span class="doc">dihedral_style opls</span></a> - OPLS dihedral</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.</p>
<p>Most dihedral styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. 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.
The doc pages for individual dihedral potentials tell if it is part of
a package.</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>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>dihedral_style none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>

Event Timeline

c4science · Help