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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="tip5p-water-model">
<h1><span class="section-number">8.4.5. </span>TIP5P water model<a class="headerlink" href="#tip5p-water-model" title="Link to this heading"></a></h1>
<p>The five-point TIP5P rigid water model extends the <a class="reference internal" href="Howto_tip3p.html"><span class="doc">three-point
TIP3P model</span></a> by adding two additional sites L, usually
massless, where the charge associated with the oxygen atom is placed.
These sites L are located at a fixed distance away from the oxygen atom,
forming a tetrahedral angle that is rotated by 90 degrees from the HOH
plane. Those sites thus somewhat approximate lone pairs of the oxygen
and consequently improve the water structure to become even more
“tetrahedral” in comparison to the <a class="reference internal" href="Howto_tip4p.html"><span class="doc">four-point TIP4P model</span></a>.</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 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>A TIP5P model <em>must</em> be run using a <a class="reference internal" href="fix_rigid.html"><span class="doc">rigid fix</span></a> since
there is no other option to keep this kind of structure rigid in LAMMPS.
In order to avoid that LAMMPS produces an error due to the massless L
sites, those need to be assigned a tiny non-zero mass.</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 a the TIP5P model with a cutoff <a class="reference internal" href="#mahoney"><span class="std std-ref">(Mahoney)</span></a> and the TIP5P-E model <a class="reference internal" href="#rick"><span class="std std-ref">(Rick)</span></a> for use with a
long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 50.0%" />
<col style="width: 25.0%" />
<col style="width: 25.0%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Parameter</p></th>
<th class="head"><p>TIP5P</p></th>
<th class="head"><p>TIP5P-E</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>
</tr>
<tr class="row-odd"><td><p>H mass (amu)</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>0.0</p></td>
<td><p>0.0</p></td>
</tr>
<tr class="row-odd"><td><p>L charge (<span class="math notranslate nohighlight">\(e\)</span>)</p></td>
<td><p>-0.241</p></td>
<td><p>-0.241</p></td>
</tr>
<tr class="row-even"><td><p>H charge (<span class="math notranslate nohighlight">\(e\)</span>)</p></td>
<td><p>0.241</p></td>
<td><p>0.241</p></td>
</tr>
<tr class="row-odd"><td><p>LJ <span class="math notranslate nohighlight">\(\epsilon\)</span> of OO (kcal/mole)</p></td>
<td><p>0.1600</p></td>
<td><p>0.1780</p></td>
</tr>
<tr class="row-even"><td><p>LJ <span class="math notranslate nohighlight">\(\sigma\)</span> of OO (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>3.1200</p></td>
<td><p>3.0970</p></td>
</tr>
<tr class="row-odd"><td><p>LJ <span class="math notranslate nohighlight">\(\epsilon\)</span> of HH, LL, OH, OL, HL (kcal/mole)</p></td>
<td><p>0.0</p></td>
<td><p>0.0</p></td>
</tr>
<tr class="row-even"><td><p>LJ <span class="math notranslate nohighlight">\(\sigma\)</span> of HH, LL, OH, OL, HL (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>1.0</p></td>
<td><p>1.0</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>
</tr>
<tr class="row-even"><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>
</tr>
<tr class="row-odd"><td><p>OL distance (<span class="math notranslate nohighlight">\(\AA\)</span>)</p></td>
<td><p>0.70</p></td>
<td><p>0.70</p></td>
</tr>
<tr class="row-even"><td><p><span class="math notranslate nohighlight">\(\theta_0\)</span> of LOL angle</p></td>
<td><p>109.47<span class="math notranslate nohighlight">\(^{\circ}\)</span></p></td>
<td><p>109.47<span class="math notranslate nohighlight">\(^{\circ}\)</span></p></td>
</tr>
</tbody>
</table>
<p>Below is the code for a LAMMPS input file for setting up a simulation of
TIP5P water with a molecule file. Because of using <a class="reference internal" href="fix_rigid.html"><span class="doc">fix
rigid/small</span></a> no bonds need to be defined and thus no extra
storage needs to be reserved for them, but we need to either switch to
atom style full or use <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom mol</span></a>
so that fix rigid/small can identify rigid bodies by their molecule ID.
Also a <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify exclude</span></a> command is added to
exclude computing intramolecular non-bonded interactions, since those
are removed by the rigid fix anyway:</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">charge</span>
<span class="k">atom_modify</span><span class="w"> </span><span class="n">map</span><span class="w"> </span><span class="n">array</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">3</span><span class="w"> </span><span class="nv nv-Identifier">box</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">mass</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">1.0e-100</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">0.160</span><span class="w"> </span><span class="m">3.12</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">pair_coeff</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="m">1.0</span>
<span class="k">fix </span><span class="nv nv-Identifier">mol</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">property</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">mol</span>
<span class="k">molecule</span><span class="w"> </span><span class="n">water</span><span class="w"> </span><span class="n">tip5p.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">neigh_modify</span><span class="w"> </span><span class="n">exclude</span><span class="w"> </span><span class="n">molecule</span><span class="o">/</span><span class="n">intra</span><span class="w"> </span><span class="n">all</span>
<span class="k">timestep</span><span class="w"> </span><span class="m">0.5</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">rigid</span><span class="o">/</span><span class="n">small</span><span class="w"> </span><span class="n">molecule</span><span class="w"> </span><span class="n">langevin</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">50.0</span><span class="w"> </span><span class="m">235664</span>
<span class="k">reset_timestep</span><span class="w"> </span><span class="m">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">density</span><span class="w"> </span><span class="n">pe</span><span class="w"> </span><span class="n">ke</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">tip5p.data</span><span class="w"> </span><span class="n">nocoeff</span>
</pre></div>
</div>
<div class="highlight-none notranslate" id="tip5p-molecule"><div class="highlight"><pre><span></span># Water molecule. Explicit TIP5P geometry for use with fix rigid
5 atoms
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
4 0.00000 -0.46971 0.57154
5 0.00000 -0.46971 -0.57154
Types
1 1 # O
2 2 # H
3 2 # H
4 3 # L
5 3 # L
Charges
1 0.000
2 0.241
3 0.241
4 -0.241
5 -0.241
</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="mahoney"><strong>(Mahoney)</strong> Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)</p>
<p id="rick"><strong>(Rick)</strong> Rick, J Chem Phys 120, 6085 (2004)</p>
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