Homec4science
Diffusion lammps (master) Browse

lammps/doc/html/pair_charmm.html
fe49cbe4cc1fmaster

Last Change
Raw File

pair_charmm.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>pair_style lj/charmm/coul/charmm 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>pair_style lj/charmm/coul/charmm 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="pair-style-lj-charmm-coul-charmm-command">
<span id="index-0"></span><h1>pair_style lj/charmm/coul/charmm command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-charmm-omp-command">
<h1>pair_style lj/charmm/coul/charmm/omp command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-command">
<h1>pair_style lj/charmm/coul/charmm/implicit command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-omp-command">
<h1>pair_style lj/charmm/coul/charmm/implicit/omp command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-command">
<h1>pair_style lj/charmm/coul/long command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-gpu-command">
<h1>pair_style lj/charmm/coul/long/gpu command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-intel-command">
<h1>pair_style lj/charmm/coul/long/intel command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-opt-command">
<h1>pair_style lj/charmm/coul/long/opt command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-omp-command">
<h1>pair_style lj/charmm/coul/long/omp command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-msm-command">
<h1>pair_style lj/charmm/coul/msm command</h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-msm-omp-command">
<h1>pair_style lj/charmm/coul/msm/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/charmm/coul/charmm</em> or <em>lj/charmm/coul/charmm/implicit</em> or <em>lj/charmm/coul/long</em> or <em>lj/charmm/coul/msm</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/charmm/coul/charmm</em> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<em>lj/charmm/coul/charmm/implicit</em> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<em>lj/charmm/coul/long</em> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
<em>lj/charmm/coul/msm</em> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">implicit</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">implicit</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>lj/charmm</em> styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a widely
used potential in the <a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> MD code.
See <a class="reference internal" href="#pair-mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
field.</p>
<img alt="_images/pair_charmm.jpg" class="align-center" src="_images/pair_charmm.jpg" />
<p>Both the LJ and Coulombic terms require an inner and outer cutoff.
They can be the same for both formulas or different depending on
whether 2 or 4 arguments are used in the pair_style command. In each
case, the inner cutoff distance must be less than the outer cutoff.
It it typical to make the difference between the 2 cutoffs about 1.0
Angstrom.</p>
<p>Style <em>lj/charmm/coul/charmm/implicit</em> computes the same formulas as
style <em>lj/charmm/coul/charmm</em> except that an additional 1/r term is
included in the Coulombic formula. The Coulombic energy thus varies
as 1/r^2. This is effectively a distance-dependent dielectric term
which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).</p>
<p>Styles <em>lj/charmm/coul/long</em> and <em>lj/charmm/coul/msm</em> compute the same
formulas as style <em>lj/charmm/coul/charmm</em> except that an additional
damping factor is applied to the Coulombic term, as described for the
<a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a> pair styles. Only one Coulombic cutoff is
specified for <em>lj/charmm/coul/long</em> and <em>lj/charmm/coul/msm</em>; if only
2 arguments are used in the pair_style command, then the outer LJ
cutoff is used as the single Coulombic cutoff.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
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, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>epsilon_14 (energy units)</li>
<li>sigma_14 (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.</p>
<p>The latter 2 coefficients are optional. If they are specified, they
are used in the LJ formula between 2 atoms of these types which are
also first and fourth atoms in any dihedral. No cutoffs are specified
because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.</p>
<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>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
mixed. The default mix value is <em>arithmetic</em> to coincide with the
usual settings for the CHARMM force field. See the &#8220;pair_modify&#8221;
command for details.</p>
<p>None of the lj/charmm pair styles support the
<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.</p>
<p>The <em>lj/charmm/coul/long</em> style supports the
<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> table option since it can tabulate the
short-range portion of the long-range Coulombic interaction.</p>
<p>None of the lj/charmm pair styles support the
<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> tail option for adding long-range tail
corrections to energy and pressure, since the Lennard-Jones portion of
the pair interaction is smoothed to 0.0 at the cutoff.</p>
<p>All of the lj/charmm pair styles write their information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The lj/charmm/coul/long pair style supports the use of the <em>inner</em>,
<em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a>
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the <em>pair</em> keyword of run_style respa. See the
<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a> command for details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The <em>lj/charmm/coul/charmm</em> and <em>lj/charmm/coul/charmm/implicit</em>
styles are part of the MOLECULE package. The <em>lj/charmm/coul/long</em>
style is part of the KSPACE package. 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. Note that
the MOLECULE and KSPACE packages are installed by default.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="pair-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</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>
c4science · Help