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<li class="breadcrumb-item active"><span class="section-number">8.4.6. </span>SPC water model</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="spc-water-model">
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<h1><span class="section-number">8.4.6. </span>SPC water model<a class="headerlink" href="#spc-water-model" title="Link to this heading"></a></h1>
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<p>The SPC water model specifies a 3-site rigid water molecule with
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charges and Lennard-Jones parameters assigned to each of the three atoms.
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In LAMMPS the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command can be used to hold
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the two O-H bonds and the H-O-H angle rigid. A bond style of
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<em>harmonic</em> and an angle style of <em>harmonic</em> or <em>charmm</em> should also be
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used.</p>
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<p>These are the additional parameters (in real units) to set for O and H
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atoms and the water molecule to run a rigid SPC model.</p>
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<div class="line-block">
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<div class="line">O mass = 15.9994</div>
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<div class="line">H mass = 1.008</div>
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<div class="line">O charge = -0.820</div>
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<div class="line">H charge = 0.410</div>
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<div class="line">LJ <span class="math notranslate nohighlight">\(\epsilon\)</span> of OO = 0.1553</div>
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<div class="line">LJ <span class="math notranslate nohighlight">\(\sigma\)</span> of OO = 3.166</div>
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<div class="line">LJ <span class="math notranslate nohighlight">\(\epsilon\)</span>, <span class="math notranslate nohighlight">\(\sigma\)</span> of OH, HH = 0.0</div>
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<div class="line"><span class="math notranslate nohighlight">\(r_0\)</span> of OH bond = 1.0</div>
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<div class="line"><span class="math notranslate nohighlight">\(\theta_0\)</span> of HOH angle = 109.47<span class="math notranslate nohighlight">\(^{\circ}\)</span></div>
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</div>
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<p>Note that as originally proposed, the SPC model was run with a 9
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Angstrom cutoff for both LJ and Coulomb terms. It can also be used
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with long-range electrostatic solvers (e.g. Ewald or PPPM in LAMMPS)
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without changing any of the parameters above, although it becomes
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a different model in that mode of usage.</p>
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<p>The SPC/E (extended) water model is the same, except
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the partial charge assignments change:</p>
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<div class="line-block">
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<div class="line">O charge = -0.8476</div>
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<div class="line">H charge = 0.4238</div>
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</div>
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<p>See the <a class="reference internal" href="#howto-berendsen"><span class="std std-ref">(Berendsen2)</span></a> reference for more details on both
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the SPC and SPC/E models.</p>
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<p>Below is the code for a LAMMPS input file and a molecule file
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(<code class="docutils literal notranslate"><span class="pre">spce.mol</span></code>) of SPC/E water for use with the <a class="reference internal" href="molecule.html"><span class="doc">molecule command</span></a> demonstrating how to set up a small bulk water system for
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SPC/E with rigid bonds.</p>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">units</span><span class="w"> </span><span class="n">real</span>
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<span class="k">atom_style</span><span class="w"> </span><span class="n">full</span>
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<span class="k">region </span><span class="nv nv-Identifier">box</span><span class="w"> </span><span class="n">block</span><span class="w"> </span><span class="o">-</span><span class="m">5</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="o">-</span><span class="m">5</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="o">-</span><span class="m">5</span><span class="w"> </span><span class="m">5</span>
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<span class="k">create_box </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">box</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">types</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">angle</span><span class="o">/</span><span class="n">types</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="o">&</span>
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<span class="w"> </span><span class="n">extra</span><span class="o">/</span><span class="n">bond</span><span class="o">/</span><span class="n">per</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="n">extra</span><span class="o">/</span><span class="n">angle</span><span class="o">/</span><span class="n">per</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">extra</span><span class="o">/</span><span class="n">special</span><span class="o">/</span><span class="n">per</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="m">2</span>
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<span class="k">mass</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">15.9994</span>
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<span class="k">mass</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">1.008</span>
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<span class="k">pair_style</span><span class="w"> </span><span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span><span class="w"> </span><span class="m">10.0</span>
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<span class="k">pair_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">0.1553</span><span class="w"> </span><span class="m">3.166</span>
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<span class="k">pair_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.0</span>
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<span class="k">pair_coeff</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.0</span>
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<span class="k">bond_style</span><span class="w"> </span><span class="n">zero</span>
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<span class="k">bond_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1.0</span>
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<span class="k">angle_style</span><span class="w"> </span><span class="n">zero</span>
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<span class="k">angle_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">109.47</span>
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<span class="k">molecule</span><span class="w"> </span><span class="n">water</span><span class="w"> </span><span class="n">spce.mol</span>
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<span class="k">create_atoms</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="n">random</span><span class="w"> </span><span class="m">33</span><span class="w"> </span><span class="m">34564</span><span class="w"> </span><span class="n">NULL</span><span class="w"> </span><span class="n">mol</span><span class="w"> </span><span class="n">water</span><span class="w"> </span><span class="m">25367</span><span class="w"> </span><span class="n">overlap</span><span class="w"> </span><span class="m">1.33</span>
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<span class="k">timestep</span><span class="w"> </span><span class="m">1.0</span>
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<span class="k">fix </span><span class="nv nv-Identifier">rigid</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">shake</span><span class="w"> </span><span class="m">0.0001</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">10000</span><span class="w"> </span><span class="n">b</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="m">1</span>
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<span class="k">minimize</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="m">10000</span>
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<span class="k">velocity </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">create</span><span class="w"> </span><span class="m">300.0</span><span class="w"> </span><span class="m">5463576</span>
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<span class="k">fix </span><span class="nv nv-Identifier">integrate</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">nvt</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="m">300.0</span><span class="w"> </span><span class="m">300.0</span><span class="w"> </span><span class="m">100.0</span>
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<span class="k">thermo_style</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="n">step</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="n">press</span><span class="w"> </span><span class="n">etotal</span><span class="w"> </span><span class="n">density</span><span class="w"> </span><span class="n">pe</span><span class="w"> </span><span class="n">ke</span>
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<span class="k">thermo</span><span class="w"> </span><span class="m">1000</span>
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<span class="k">run</span><span class="w"> </span><span class="m">20000</span><span class="w"> </span><span class="n">upto</span>
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<span class="k">write_data </span><span class="nv nv-Identifier">spce.data</span><span class="w"> </span><span class="n">nocoeff</span>
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</pre></div>
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</div>
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<div class="highlight-none notranslate" id="spce-molecule"><div class="highlight"><pre><span></span># Water molecule. SPC/E geometry
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3 atoms
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2 bonds
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1 angles
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Coords
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1 0.00000 -0.06461 0.00000
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2 0.81649 0.51275 0.00000
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3 -0.81649 0.51275 0.00000
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Types
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1 1 # O
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2 2 # H
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3 2 # H
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Charges
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1 -0.8476
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2 0.4238
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3 0.4238
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Bonds
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1 1 1 2
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2 1 1 3
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Angles
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1 1 2 1 3
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Shake Flags
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1 1
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2 1
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3 1
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Shake Atoms
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1 1 2 3
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2 1 2 3
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3 1 2 3
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Shake Bond Types
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1 1 1 1
|
|
2 1 1 1
|
|
3 1 1 1
|
|
|
|
Special Bond Counts
|
|
|
|
1 2 0 0
|
|
2 1 1 0
|
|
3 1 1 0
|
|
|
|
Special Bonds
|
|
|
|
1 2 3
|
|
2 1 3
|
|
3 1 2
|
|
</pre></div>
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</div>
|
|
<p>Wikipedia also has a nice article on <a class="reference external" href="https://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
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<hr class="docutils" />
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<p id="howto-berendsen"><strong>(Berendsen2)</strong> Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).</p>
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