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471 lines
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<li>pair_style lj/cut/soft command</li>
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<div class="section" id="pair-style-lj-cut-soft-command">
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<span id="index-0"></span><h1>pair_style lj/cut/soft command<a class="headerlink" href="#pair-style-lj-cut-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-cut-soft-omp-command">
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<h1>pair_style lj/cut/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-soft-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-cut-coul-cut-soft-command">
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<h1>pair_style lj/cut/coul/cut/soft command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-cut-coul-cut-soft-omp-command">
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<h1>pair_style lj/cut/coul/cut/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-soft-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-cut-coul-long-soft-command">
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<h1>pair_style lj/cut/coul/long/soft command<a class="headerlink" href="#pair-style-lj-cut-coul-long-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-cut-coul-long-soft-omp-command">
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<h1>pair_style lj/cut/coul/long/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-long-soft-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-cut-tip4p-long-soft-command">
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<h1>pair_style lj/cut/tip4p/long/soft command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-cut-tip4p-long-soft-omp-command">
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<h1>pair_style lj/cut/tip4p/long/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-soft-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-charmm-coul-long-soft-command">
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<h1>pair_style lj/charmm/coul/long/soft command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-charmm-coul-long-soft-omp-command">
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<h1>pair_style lj/charmm/coul/long/soft/omp command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-soft-omp-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-coul-cut-soft-command">
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<h1>pair_style coul/cut/soft command<a class="headerlink" href="#pair-style-coul-cut-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-coul-cut-soft-omp-command">
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<h1>pair_style coul/cut/soft/omp command<a class="headerlink" href="#pair-style-coul-cut-soft-omp-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-coul-long-soft-command">
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<h1>pair_style coul/long/soft command<a class="headerlink" href="#pair-style-coul-long-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-coul-long-soft-omp-command">
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<h1>pair_style coul/long/soft/omp command<a class="headerlink" href="#pair-style-coul-long-soft-omp-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-tip4p-long-soft-command">
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<h1>pair_style tip4p/long/soft command<a class="headerlink" href="#pair-style-tip4p-long-soft-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-tip4p-long-soft-omp-command">
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<h1>pair_style tip4p/long/soft/omp command<a class="headerlink" href="#pair-style-tip4p-long-soft-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/cut/soft</em> or <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> or <em>lj/cut/tip4p/long/soft</em> or <em>lj/charmm/coul/long/soft</em> or <em>coul/cut/soft</em> or <em>coul/long/soft</em> or <em>tip4p/long/soft</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/cut/soft</em> args = n alpha_lj cutoff
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n, alpha_LJ = parameters of soft-core potential
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cutoff = global cutoff for Lennard-Jones interactions (distance units)
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<em>lj/cut/coul/cut/soft</em> args = n alpha_LJ alpha_C cutoff (cutoff2)
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n, alpha_LJ, alpha_C = parameters of soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<em>lj/cut/coul/long/soft</em> args = n alpha_LJ alpha_C cutoff
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<em>lj/cut/tip4p/long/soft</em> args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<em>lj/charmm/coul/long/soft</em> args = n alpha_LJ alpha_C inner outer (cutoff)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
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<em>coul/cut/soft</em> args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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<em>coul/long/soft</em> args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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<em>tip4p/long/soft</em> args = otype htype btype atype qdist n alpha_C cutoff
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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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/cut/soft 2.0 0.5 9.5
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 1.0 9.5
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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/cut/coul/cut/soft 2.0 0.5 10.0 9.5
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pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 0.5 10.0
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pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
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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/cut/coul/long/soft 2.0 0.5 10.0 9.5
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pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 0.0 10.0
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pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
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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/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
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pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
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pair_coeff * * 0.155 3.1536 1.0
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pair_coeff 1 1 0.155 3.1536 1.0 9.5
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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/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
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pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
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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 coul/long/soft 1.0 10.0 9.5
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 9.5
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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 tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 9.5
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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/cut/soft</em> style and substyles compute the 12/6 Lennard-Jones
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and Coulomb potential modified by a soft core, in order to avoid
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singularities during free energy calculations when sites are created
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or anihilated <a class="reference internal" href="#beutler"><span>(Beutler)</span></a>,</p>
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<img alt="_images/pair_lj_soft.jpg" class="align-center" src="_images/pair_lj_soft.jpg" />
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<p>Coulomb interactions are also damped with a soft core at short
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distance,</p>
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<img alt="_images/pair_coul_soft.jpg" class="align-center" src="_images/pair_coul_soft.jpg" />
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<p>In the Coulomb part C is an energy-conversion constant, q_i and q_j
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are the charges on the 2 atoms, and epsilon is the dielectric constant
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which can be set by the <a class="reference internal" href="dielectric.html"><em>dielectric</em></a> command.</p>
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<p>The coefficient lambda is an activation parameter. When lambda = 1 the
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pair potentiel is identical to a Lennard-Jones term or a Coulomb term
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or a combination of both. When lambda = 0 the interactions are
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deactivated. The transition between these two extrema is smoothed by a
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soft repulsive core in order to avoid singularities in potential
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energy and forces when sites are created or anihilated and can overlap
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<a class="reference internal" href="#beutler"><span>(Beutler)</span></a>.</p>
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<p>The paratemers n, alpha_LJ and alpha_C are set in the
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<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, before the cutoffs. Usual
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choices for the exponent are n = 2 or n = 1. For the remaining
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coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
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appropriate choices. Plots of the LJ and Coulomb terms are shown
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below, for lambda ranging from 1 to 0 every 0.1.</p>
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<img alt="_images/lj_soft.jpg" class="align-center" src="_images/lj_soft.jpg" />
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<img alt="_images/coul_soft.jpg" class="align-center" src="_images/coul_soft.jpg" />
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<p>For the <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> pair styles,
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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>lambda (activation parameter between 0 and 1)</li>
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<li>cutoff1 (distance units)</li>
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<li>cutoff2 (distance units)</li>
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</ul>
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<p>The latter two coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair. You cannot specify 2 cutoffs for style <em>lj/cut/soft</em>,
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since it has no Coulombic terms. For the <em>coul/cut/soft</em> and
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<em>coul/long/soft</em> only lambda and the optional cutoff2 are to be
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specified.</p>
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<p>Style <em>lj/cut/tip4p/long/soft</em> implements a soft-core version of the
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TIP4P water model. The usage of this pair style is documented in the
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<a class="reference internal" href="pair_lj.html"><em>pair_lj</em></a> styles. The soft-core version introduces the
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lambda parameter to the list of arguments, after epsilon and sigma in
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the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. The paratemers n, alpha_LJ
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and alpha_C are set in the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command,
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before the cutoffs.</p>
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<p>Style <em>lj/charmm/coul/long/soft</em> implements a soft-core version of the
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CHARMM version of LJ interactions with an additional switching
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function S(r) that ramps the energy and force smoothly to zero between
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an inner and outer cutoff. The usage of this pair style is documented
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in the <a class="reference internal" href="pair_charmm.html"><em>pair_charmm</em></a> styles. The soft-core version
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introduces the lambda parameter to the list of arguments, after
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epsilon and sigma in the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command (and
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before the optional eps14 and sigma14). The paratemers n,
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alpha_LJ and alpha_C are set in the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>
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command, before the cutoffs.</p>
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<p>The <em>coul/cut/soft</em>, <em>coul/long/soft</em> and <em>tip4p/long/soft</em> substyles
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are designed to be combined with other pair potentials via the
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<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command. This is because
|
|
they have no repulsive core. Hence, if used by themselves, there will
|
|
be no repulsion to keep two oppositely charged particles from
|
|
overlapping each other. In this case, if lambda = 1, a singularity may
|
|
occur. These substyles are suitable to represent charges embedded in
|
|
the Lennard-Jones radius of another site (for example hydrogen atoms
|
|
in several water models).</p>
|
|
<p>NOTES: When using the core-softed Coulomb potentials with long-range
|
|
solvers (<em>coul/long/soft</em>, <em>lj/cut/coul/long/soft</em>, etc.) in a free
|
|
energy calculation in which sites holding electrostatic charges are
|
|
being created or anihilated (using <a class="reference internal" href="fix_adapt_fep.html"><em>fix_adapt/fep</em></a>
|
|
and <a class="reference internal" href="compute_fep.html"><em>compute_fep</em></a>) it is important to adapt both the
|
|
lambda activation parameter (from 0 to 1, or the reverse) and the
|
|
value of the charge (from 0 to its final value, or the reverse). This
|
|
ensures that long-range electrostatic terms (kspace) are correct. It
|
|
is not necessary to use core-softed Coulomb potentials if the van der
|
|
Waals site is present during the free-energy route, thus avoiding
|
|
overlap of the charges. Examples are provided in the LAMMPS source
|
|
directory tree, under examples/USER/fep.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
|
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</p>
|
|
<hr class="docutils" />
|
|
<p><strong>Mixing, shift, tail correction, restart info</strong>:</p>
|
|
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
|
and cutoff distance for this pair style can be mixed.
|
|
The default mix value is <em>geometric</em>. See the “pair_modify” command
|
|
for details.</p>
|
|
<p>These pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
|
|
option for the energy of the Lennard-Jones portion of the pair
|
|
interaction.</p>
|
|
<p>These pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail
|
|
option for adding a long-range tail correction to the energy and
|
|
pressure for the Lennard-Jones portion of the pair interaction.</p>
|
|
<p>These pair styles write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
|
|
to be specified in an input script that reads a restart file.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>To avoid division by zero do not set sigma = 0; use the lambda
|
|
parameter instead to activate/deactivate interactions, or use
|
|
epsilon = 0 and sigma = 1. Alternatively, when sites do not
|
|
interact though the Lennard-Jones term the <em>coul/long/soft</em> or
|
|
similar substyle can be used via the
|
|
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command.</p>
|
|
<hr class="docutils" />
|
|
<p>All of the plain <em>soft</em> pair styles are part of the USER-FEP package.
|
|
The <em>long</em> styles also requires the KSPACE package to be installed.
|
|
They are only 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>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a>,
|
|
<a class="reference internal" href="fix_adapt_fep.html"><em>fix_adapt/fep</em></a>, <a class="reference internal" href="compute_fep.html"><em>compute_fep</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="beutler"><strong>(Beutler)</strong> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
|
|
Phys Lett, 222, 529 (1994).</p>
|
|
</div>
|
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