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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="tip3p-water-model">
<h1><span class="section-number">8.4.3. </span>TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Link to this heading"></a></h1>
<p>The TIP3P water model as implemented in CHARMM <a class="reference internal" href="#howto-tip3p"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with charges and
Lennard-Jones parameters assigned to each of the three atoms.</p>
<p>A suitable pair style with cutoff Coulomb would be:</p>
<ul class="simple">
<li><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">pair_style lj/cut/coul/cut</span></a></p></li>
</ul>
<p>or these commands for a long-range Coulomb model:</p>
<ul class="simple">
<li><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">pair_style lj/cut/coul/long</span></a></p></li>
<li><p><a class="reference internal" href="pair_fep_soft.html"><span class="doc">pair_style lj/cut/coul/long/soft</span></a></p></li>
<li><p><a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm</span></a></p></li>
<li><p><a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm/disp</span></a></p></li>
</ul>
<p>In LAMMPS the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake or fix rattle</span></a> command can be
used to hold the two O-H bonds and the H-O-H angle rigid. A bond style
of <a class="reference internal" href="bond_harmonic.html"><span class="doc">harmonic</span></a> and an angle style of <a class="reference internal" href="angle_harmonic.html"><span class="doc">harmonic</span></a> or <a class="reference internal" href="angle_charmm.html"><span class="doc">charmm</span></a> should also be used.
In case of rigid bonds also bond style <a class="reference internal" href="bond_zero.html"><span class="doc">zero</span></a> and angle
style <a class="reference internal" href="angle_zero.html"><span class="doc">zero</span></a> can be used.</p>
<p>The table below lists the force field parameters (in real <a class="reference internal" href="units.html"><span class="doc">units</span></a>) to for the water molecule atoms to run a rigid or flexible
TIP3P-CHARMM model with a cutoff, the original 1983 TIP3P model
<a class="reference internal" href="#jorgensen1"><span class="std std-ref">(Jorgensen)</span></a>, or a TIP3P model with parameters
optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
<a class="reference internal" href="#price1"><span class="std std-ref">(Price)</span></a>. The K values can be used if a flexible TIP3P
model (without fix shake) is desired, for rigid bonds/angles they are
ignored.</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 38.0%" />
<col style="width: 22.0%" />
<col style="width: 20.0%" />
<col style="width: 20.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Parameter</p></th>
<th class="head"><p>TIP3P-CHARMM</p></th>
<th class="head"><p>TIP3P (original)</p></th>
<th class="head"><p>TIP3P (Ewald)</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>O mass (amu)</p></td>
<td><p>15.9994</p></td>
<td><p>15.9994</p></td>
<td><p>15.9994</p></td>
</tr>
<tr class="row-odd"><td><p>H mass (amu)</p></td>
<td><p>1.008</p></td>
<td><p>1.008</p></td>
<td><p>1.008</p></td>
</tr>
<tr class="row-even"><td><p>O charge (<span class="math notranslate nohighlight">\(e\)</span>)</p></td>
<td><p>-0.834</p></td>
<td><p>-0.834</p></td>
<td><p>-0.834</p></td>
</tr>
<tr class="row-odd"><td><p>H charge (<span class="math notranslate nohighlight">\(e\)</span>)</p></td>
<td><p>0.417</p></td>
<td><p>0.417</p></td>
<td><p>0.417</p></td>
</tr>
<tr class="row-even"><td><p>LJ <span class="math notranslate nohighlight">\(\epsilon\)</span> of OO (kcal/mole)</p></td>
<td><p>0.1521</p></td>
<td><p>0.1521</p></td>
<td><p>0.1020</p></td>
</tr>
<tr class="row-odd"><td><p>LJ <span class="math notranslate nohighlight">\(\sigma\)</span> of OO (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>3.1507</p></td>
<td><p>3.1507</p></td>
<td><p>3.188</p></td>
</tr>
<tr class="row-even"><td><p>LJ <span class="math notranslate nohighlight">\(\epsilon\)</span> of HH (kcal/mole)</p></td>
<td><p>0.0460</p></td>
<td><p>0.0</p></td>
<td><p>0.0</p></td>
</tr>
<tr class="row-odd"><td><p>LJ <span class="math notranslate nohighlight">\(\sigma\)</span> of HH (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>0.4</p></td>
<td><p>1.0</p></td>
<td><p>1.0</p></td>
</tr>
<tr class="row-even"><td><p>LJ <span class="math notranslate nohighlight">\(\epsilon\)</span> of OH (kcal/mole)</p></td>
<td><p>0.0836</p></td>
<td><p>0.0</p></td>
<td><p>0.0</p></td>
</tr>
<tr class="row-odd"><td><p>LJ <span class="math notranslate nohighlight">\(\sigma\)</span> of OH (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>1.7753</p></td>
<td><p>1.0</p></td>
<td><p>1.0</p></td>
</tr>
<tr class="row-even"><td><p>K of OH bond (kcal/mole/<span class="math notranslate nohighlight">\(\AA^2\)</span>)</p></td>
<td><p>450</p></td>
<td><p>450</p></td>
<td><p>450</p></td>
</tr>
<tr class="row-odd"><td><p><span class="math notranslate nohighlight">\(r_0\)</span> of OH bond (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>0.9572</p></td>
<td><p>0.9572</p></td>
<td><p>0.9572</p></td>
</tr>
<tr class="row-even"><td><p>K of HOH angle (kcal/mole)</p></td>
<td><p>55.0</p></td>
<td><p>55.0</p></td>
<td><p>55.0</p></td>
</tr>
<tr class="row-odd"><td><p><span class="math notranslate nohighlight">\(\theta_0\)</span> of HOH angle</p></td>
<td><p>104.52<span class="math notranslate nohighlight">\(^{\circ}\)</span></p></td>
<td><p>104.52<span class="math notranslate nohighlight">\(^{\circ}\)</span></p></td>
<td><p>104.52<span class="math notranslate nohighlight">\(^{\circ}\)</span></p></td>
</tr>
</tbody>
</table>
<p>Below is the code for a LAMMPS input file and a molecule file
(<code class="docutils literal notranslate"><span class="pre">tip3p.mol</span></code>) of TIP3P 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
TIP3P with rigid bonds.</p>
<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>
<span class="k">atom_style</span><span class="w"> </span><span class="n">full</span>
<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>
<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">&amp;</span>
<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>
<span class="k">mass</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">15.9994</span>
<span class="k">mass</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">1.008</span>
<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">8.0</span>
<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">0.1521</span><span class="w"> </span><span class="m">3.1507</span>
<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>
<span class="k">bond_style</span><span class="w"> </span><span class="n">zero</span>
<span class="k">bond_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">0.9574</span>
<span class="k">angle_style</span><span class="w"> </span><span class="n">zero</span>
<span class="k">angle_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">104.52</span>
<span class="k">molecule</span><span class="w"> </span><span class="n">water</span><span class="w"> </span><span class="n">tip3p.mol</span>
<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>
<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">0.001</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>
<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>
<span class="k">reset_timestep</span><span class="w"> </span><span class="m">0</span>
<span class="k">timestep</span><span class="w"> </span><span class="m">1.0</span>
<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>
<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</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">100.0</span>
<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">pe</span>
<span class="k">thermo</span><span class="w"> </span><span class="m">1000</span>
<span class="k">run</span><span class="w"> </span><span class="m">20000</span>
<span class="k">write_data </span><span class="nv nv-Identifier">tip3p.data</span><span class="w"> </span><span class="n">nocoeff</span>
</pre></div>
</div>
<div class="highlight-none notranslate" id="tip3p-molecule"><div class="highlight"><pre><span></span># Water molecule. TIP3P geometry
3 atoms
2 bonds
1 angles
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
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>
</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>
<hr class="docutils" />
<p id="howto-tip3p"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<p id="jorgensen1"><strong>(Jorgensen)</strong> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).</p>
<p id="price1"><strong>(Price)</strong> Price and Brooks, J Chem Phys, 121, 10096 (2004).</p>
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