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<title>pair_style lj/gromacs command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="pair-style-lj-gromacs-command">
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<span id="index-0"></span><h1>pair_style lj/gromacs command<a class="headerlink" href="#pair-style-lj-gromacs-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-gromacs-cuda-command">
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<h1>pair_style lj/gromacs/cuda command<a class="headerlink" href="#pair-style-lj-gromacs-cuda-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-gromacs-gpu-command">
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<h1>pair_style lj/gromacs/gpu command<a class="headerlink" href="#pair-style-lj-gromacs-gpu-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-gromacs-omp-command">
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<h1>pair_style lj/gromacs/omp command<a class="headerlink" href="#pair-style-lj-gromacs-omp-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-gromacs-coul-gromacs-command">
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<h1>pair_style lj/gromacs/coul/gromacs command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-gromacs-coul-gromacs-cuda-command">
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<h1>pair_style lj/gromacs/coul/gromacs/cuda command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-cuda-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-gromacs-coul-gromacs-omp-command">
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<h1>pair_style lj/gromacs/coul/gromacs/omp command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-omp-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style style args
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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/gromacs</em> or <em>lj/gromacs/coul/gromacs</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/gromacs</em> args = inner outer
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inner, outer = global switching cutoffs for Lennard Jones
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<em>lj/gromacs/coul/gromacs</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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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style lj/gromacs 9.0 12.0
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pair_coeff * * 100.0 2.0
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pair_coeff 2 2 100.0 2.0 8.0 10.0
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>pair_style lj/gromacs/coul/gromacs 9.0 12.0
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pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>The <em>lj/gromacs</em> styles compute shifted LJ and Coulombic interactions
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with an 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 commonly
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used potential in the <a class="reference external" href="http://www.gromacs.org">GROMACS</a> MD code and for
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the coarse-grained models of <a class="reference internal" href="#marrink"><span>(Marrink)</span></a>.</p>
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<img alt="_images/pair_gromacs.jpg" class="align-center" src="_images/pair_gromacs.jpg" />
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<p>r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B,
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and C are computed by LAMMPS to perform the shifting and smoothing.
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The function
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S(r) is actually applied once to each term of the LJ formula and once
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to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
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depending on which pair_style is used. The boundary conditions
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applied to the smoothing function are as follows: S’(r1) = S’‘(r1) = 0,
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S(rc) = -E(rc), S’(rc) = -E’(rc), and S’‘(rc) = -E’‘(rc),
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where E(r) is the corresponding term
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in the LJ or Coulombic potential energy function.
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Single and double primes denote first and second
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derivatives with respect to r, respectively.</p>
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<p>The inner and outer cutoff for the LJ and Coulombic terms can be the
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same or different depending on whether 2 or 4 arguments are used in
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the pair_style command. The inner LJ cutoff must be > 0, but the
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inner Coulombic cutoff can be >= 0.</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"><em>pair_coeff</em></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"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></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>inner (distance units)</li>
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<li>outer (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 last 2 coefficients are optional inner and outer cutoffs for style
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<em>lj/gromacs</em>. If not specified, the global <em>inner</em> and <em>outer</em> values
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are used.</p>
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<p>The last 2 coefficients cannot be used with style
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<em>lj/gromacs/coul/gromacs</em> because this force field does not allow
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varying cutoffs for individual atom pairs; all pairs use the global
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cutoff(s) specified in the pair_style command.</p>
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<hr class="docutils" />
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<p>Styles <em>intel</em>, <em>kk</em>, with a <em>cuda</em>, <em>gpu</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"><em>Section_accelerate</em></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 USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>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>-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"><em>suffix</em></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></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 and sigma coefficients
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and cutoff distance for all of the lj/cut pair styles can be mixed.
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The default mix value is <em>geometric</em>. See the “pair_modify” command
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for details.</p>
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<p>None of the GROMACS pair styles support the
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<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option, since the Lennard-Jones
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portion of the pair interaction is already smoothed to 0.0 at the
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cutoff.</p>
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<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
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for this pair style.</p>
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<p>None of the GROMACS pair styles support the
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<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail option for adding long-range tail
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corrections to energy and pressure, since there are no corrections for
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a potential that goes to 0.0 at the cutoff.</p>
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<p>All of the GROMACS pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></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>All of the GROMACS pair styles can only be used via the <em>pair</em>
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keyword of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. They do not
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support the <em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</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<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="marrink"><strong>(Marrink)</strong> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).</p>
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