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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li>pair_style lj/charmm/coul/charmm command</li>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-command">
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<span id="index-0"></span><h1>pair_style lj/charmm/coul/charmm command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-omp-command">
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<h1>pair_style lj/charmm/coul/charmm/omp command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-command">
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<h1>pair_style lj/charmm/coul/charmm/implicit command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-omp-command">
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<h1>pair_style lj/charmm/coul/charmm/implicit/omp command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-long-command">
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<h1>pair_style lj/charmm/coul/long command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-long-gpu-command">
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<h1>pair_style lj/charmm/coul/long/gpu command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-long-intel-command">
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<h1>pair_style lj/charmm/coul/long/intel command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-long-opt-command">
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<h1>pair_style lj/charmm/coul/long/opt command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-long-omp-command">
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<h1>pair_style lj/charmm/coul/long/omp command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-msm-command">
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<h1>pair_style lj/charmm/coul/msm command</h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-msm-omp-command">
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<h1>pair_style lj/charmm/coul/msm/omp command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<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>
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</pre></div>
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</div>
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<ul class="simple">
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<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>
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<li>args = list of arguments for a particular style</li>
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</ul>
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<pre class="literal-block">
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<em>lj/charmm/coul/charmm</em> args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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<em>lj/charmm/coul/charmm/implicit</em> args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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<em>lj/charmm/coul/long</em> args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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<em>lj/charmm/coul/msm</em> args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<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>
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<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>
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<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>
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<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>
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</pre></div>
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</div>
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<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>
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<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>
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<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>
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<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>
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</pre></div>
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</div>
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<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>
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<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>
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<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>
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<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>
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</pre></div>
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</div>
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<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>
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<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>
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<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>
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<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>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>The <em>lj/charmm</em> styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a widely
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used potential in the <a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> MD code.
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See <a class="reference internal" href="#pair-mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
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field.</p>
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<img alt="_images/pair_charmm.jpg" class="align-center" src="_images/pair_charmm.jpg" />
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<p>Both the LJ and Coulombic terms require an inner and outer cutoff.
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They can be the same for both formulas or different depending on
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whether 2 or 4 arguments are used in the pair_style command. In each
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case, the inner cutoff distance must be less than the outer cutoff.
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It it typical to make the difference between the 2 cutoffs about 1.0
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Angstrom.</p>
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<p>Style <em>lj/charmm/coul/charmm/implicit</em> computes the same formulas as
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style <em>lj/charmm/coul/charmm</em> except that an additional 1/r term is
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included in the Coulombic formula. The Coulombic energy thus varies
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as 1/r^2. This is effectively a distance-dependent dielectric term
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which is a simple model for an implicit solvent with additional
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screening. It is designed for use in a simulation of an unsolvated
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biomolecule (no explicit water molecules).</p>
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<p>Styles <em>lj/charmm/coul/long</em> and <em>lj/charmm/coul/msm</em> compute the same
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formulas as style <em>lj/charmm/coul/charmm</em> except that an additional
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damping factor is applied to the Coulombic term, as described for the
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<a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a> pair styles. Only one Coulombic cutoff is
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specified for <em>lj/charmm/coul/long</em> and <em>lj/charmm/coul/msm</em>; if only
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2 arguments are used in the pair_style command, then the outer LJ
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cutoff is used as the single Coulombic cutoff.</p>
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<p>The following coefficients must be defined for each pair of atoms
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types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
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above, or in the data file or restart files read by the
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<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>
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commands, or by mixing as described below:</p>
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<ul class="simple">
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<li>epsilon (energy units)</li>
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<li>sigma (distance units)</li>
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<li>epsilon_14 (energy units)</li>
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<li>sigma_14 (distance units)</li>
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</ul>
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<p>Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.</p>
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<p>The latter 2 coefficients are optional. If they are specified, they
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are used in the LJ formula between 2 atoms of these types which are
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also first and fourth atoms in any dihedral. No cutoffs are specified
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because this CHARMM force field does not allow varying cutoffs for
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individual atom pairs; all pairs use the global cutoff(s) specified in
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the pair_style command.</p>
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<hr class="docutils" />
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<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.</p>
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<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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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>
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<p>You can specify the accelerated styles explicitly in your input script
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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
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use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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<hr class="docutils" />
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<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
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<p>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
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and sigma_14 coefficients for all of the lj/charmm pair styles can be
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mixed. The default mix value is <em>arithmetic</em> to coincide with the
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usual settings for the CHARMM force field. See the “pair_modify”
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command for details.</p>
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<p>None of the lj/charmm pair styles support the
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<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift option, since the Lennard-Jones
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portion of the pair interaction is smoothed to 0.0 at the cutoff.</p>
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<p>The <em>lj/charmm/coul/long</em> style supports the
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<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> table option since it can tabulate the
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short-range portion of the long-range Coulombic interaction.</p>
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<p>None of the lj/charmm pair styles support the
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<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> tail option for adding long-range tail
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corrections to energy and pressure, since the Lennard-Jones portion of
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the pair interaction is smoothed to 0.0 at the cutoff.</p>
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<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
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not need to be specified in an input script that reads a restart file.</p>
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<p>The lj/charmm/coul/long pair style supports the use of the <em>inner</em>,
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<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>
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command, meaning the pairwise forces can be partitioned by distance at
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different levels of the rRESPA hierarchy. The other styles only
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support the <em>pair</em> keyword of run_style respa. See the
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<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a> command for details.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>The <em>lj/charmm/coul/charmm</em> and <em>lj/charmm/coul/charmm/implicit</em>
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styles are part of the MOLECULE package. The <em>lj/charmm/coul/long</em>
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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>
|
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</div>
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<div class="section" id="related-commands">
|
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<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>
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