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<!DOCTYPE html>
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<li class="toctree-l1"><a class="reference internal" href="commandlines.html">Command lines</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Topology file format</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#nonbonded-potentials">Nonbonded potentials</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#lennard-jones">Lennard-Jones</a></li>
<li class="toctree-l3"><a class="reference internal" href="#tabulated-conversion">Tabulated (conversion)</a></li>
<li class="toctree-l3"><a class="reference internal" href="#tabulated-mixed-conversion">Tabulated (mixed, conversion)</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#bonded-potentials">Bonded potentials</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#harmonic-bond">Harmonic bond</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fene-bond">FENE bond</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fene-bond-with-lj-interactions-included">FENE bond with LJ interactions included</a></li>
<li class="toctree-l3"><a class="reference internal" href="#harmonic-angle">Harmonic angle</a></li>
<li class="toctree-l3"><a class="reference internal" href="#cosine-angle">Cosine angle</a></li>
<li class="toctree-l3"><a class="reference internal" href="#harmonic-n-cosine-dihedral">Harmonic n-cosine dihedral</a></li>
<li class="toctree-l3"><a class="reference internal" href="#ryckaert-bellemans-dihedral">Ryckaert Bellemans dihedral</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#bondtypes">[ bondtypes ]</a></li>
<li class="toctree-l3"><a class="reference internal" href="#angletypes">[ angletypes ]</a></li>
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<div class="section" id="topology-file-format">
<h1>Topology file format<a class="headerlink" href="#topology-file-format" title="Permalink to this headline">¶</a></h1>
<div class="section" id="nonbonded-potentials">
<h2>Nonbonded potentials<a class="headerlink" href="#nonbonded-potentials" title="Permalink to this headline">¶</a></h2>
<div class="section" id="lennard-jones">
<h3>Lennard-Jones<a class="headerlink" href="#lennard-jones" title="Permalink to this headline">¶</a></h3>
<div class="math" id="lj">
\[U(r_{ij}) = 4\epsilon\left [ \left ( \frac{\sigma}{r_{ij}} \right)^{12} - \left ( \frac{\sigma}{r_{ij}} \right)^6 \right ]\]</div>
</div>
<div class="section" id="tabulated-conversion">
<h3>Tabulated (conversion)<a class="headerlink" href="#tabulated-conversion" title="Permalink to this headline">¶</a></h3>
<p id="tc">The appropriate table is selected, based on current chemical conversion.</p>
</div>
<div class="section" id="tabulated-mixed-conversion">
<h3>Tabulated (mixed, conversion)<a class="headerlink" href="#tabulated-mixed-conversion" title="Permalink to this headline">¶</a></h3>
<p>Arithmetic mixing of two tabulated potentials</p>
<p><strong>Input</strong></p>
<blockquote>
<div><ul class="simple">
<li>tab1: first tabulated potential</li>
<li>tab2: second tabulated potential</li>
<li>type: the type of particles to count in order to calculate conversion</li>
<li>total_number: the total expected number of particles of given type <strong>M</strong></li>
</ul>
</div></blockquote>
<p>The conversion is defined as:</p>
<div class="math">
\[\Phi = \frac{N_{type}}{M}\]</div>
<p>And the effective potential:</p>
<div class="math">
\[U(r_{ij}) = \Phi U^{tab1} + (1-\Phi) U^{tab2}\]</div>
</div>
</div>
<div class="section" id="bonded-potentials">
<h2>Bonded potentials<a class="headerlink" href="#bonded-potentials" title="Permalink to this headline">¶</a></h2>
<div class="section" id="harmonic-bond">
<h3>Harmonic bond<a class="headerlink" href="#harmonic-bond" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eq1">
\[U(r) = \frac{1}{2}K(r-r_0)^2\]</div>
</div>
<div class="section" id="fene-bond">
<h3>FENE bond<a class="headerlink" href="#fene-bond" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eqfene">
\[U(r) = -\frac{1}{2} K b^2 log \left( 1 - \frac{r^2}{b^2} \right)\]</div>
</div>
<div class="section" id="fene-bond-with-lj-interactions-included">
<h3>FENE bond with LJ interactions included<a class="headerlink" href="#fene-bond-with-lj-interactions-included" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eqfenelj">
\[U(r) = -\frac{1}{2} K b^2 log \left( 1 - \frac{r^2}{b^2} \right) + 4\epsilon\left [ \left ( \frac{\sigma}{r_{ij}} \right)^{12} - \left ( \frac{\sigma}{r_{ij}} \right)^6 \right ]\]</div>
</div>
<div class="section" id="harmonic-angle">
<h3>Harmonic angle<a class="headerlink" href="#harmonic-angle" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eq2">
\[U(\theta) = \frac{1}{2} K(\theta - \theta_0)^2\]</div>
</div>
<div class="section" id="cosine-angle">
<h3>Cosine angle<a class="headerlink" href="#cosine-angle" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eq3">
\[U(\theta) = \frac{1}{2} K(1.0 + cos(\theta - \theta_0))\]</div>
</div>
<div class="section" id="harmonic-n-cosine-dihedral">
<h3>Harmonic n-cosine dihedral<a class="headerlink" href="#harmonic-n-cosine-dihedral" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eq4">
\[U(\phi) = K(1 + cos(multiplicity*\phi - \phi_0));\]</div>
</div>
<div class="section" id="ryckaert-bellemans-dihedral">
<h3>Ryckaert Bellemans dihedral<a class="headerlink" href="#ryckaert-bellemans-dihedral" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eq5">
\[U(\phi) = \sum^{5}_{n=0} K_n cos^n(\phi)\]</div>
</div>
<div class="section" id="dihedral-harmonic">
<h3>Dihedral Harmonic<a class="headerlink" href="#dihedral-harmonic" title="Permalink to this headline">¶</a></h3>
<div class="math" id="eq7">
\[U(\phi) = \frac{1}{2} K (\phi - \phi_0)^2\]</div>
</div>
</div>
<div class="section" id="topology-file">
<h2>Topology file<a class="headerlink" href="#topology-file" title="Permalink to this headline">¶</a></h2>
<p>In principle, ChemLab uses GROMACS-like topology file format. However, some functional types are different.</p>
<div class="section" id="bondtypes">
<h3>[ bondtypes ]<a class="headerlink" href="#bondtypes" title="Permalink to this headline">¶</a></h3>
<table border="1" class="docutils">
<colgroup>
<col width="49%" />
<col width="10%" />
<col width="41%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Name of interaction</th>
<th class="head">func</th>
<th class="head">params</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Harmonic <a class="reference internal" href="#eq1">eq1</a></td>
<td>1</td>
<td>r0, K <a class="footnote-reference" href="#id4" id="id1">[1]</a></td>
</tr>
<tr class="row-odd"><td>FENE <a class="reference internal" href="#eqfene">eqFENE</a></td>
<td>7</td>
<td>b, K <a class="footnote-reference" href="#id4" id="id2">[1]</a></td>
</tr>
<tr class="row-even"><td>Tabulated</td>
<td>8</td>
<td>table index <a class="footnote-reference" href="#id7" id="id3">[2]</a></td>
</tr>
<tr class="row-odd"><td>FENE + LJ <a class="reference internal" href="#eqfenelj">eqFENELJ</a></td>
<td>9</td>
<td>b, K, sigma, epsilon</td>
</tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id4" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>)</em> Force constant internally divided by 2.0</td></tr>
</tbody>
</table>
</div>
<div class="section" id="angletypes">
<h3>[ angletypes ]<a class="headerlink" href="#angletypes" title="Permalink to this headline">¶</a></h3>
<table border="1" class="docutils">
<colgroup>
<col width="49%" />
<col width="10%" />
<col width="41%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Name of interaction</th>
<th class="head">func</th>
<th class="head">params</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Harmonic <a class="reference internal" href="#eq2">eq2</a></td>
<td>1</td>
<td>theta0 (deg), K <a class="footnote-reference" href="#id7" id="id5">[2]</a></td>
</tr>
<tr class="row-odd"><td>Tabulated</td>
<td>8</td>
<td>table index</td>
</tr>
<tr class="row-even"><td>Cosine <a class="reference internal" href="#eq3">eq3</a></td>
<td>11</td>
<td>theta0 (deg), K <a class="footnote-reference" href="#id7" id="id6">[2]</a></td>
</tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id7" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label">[2]</td><td><em>(<a class="fn-backref" href="#id3">1</a>, <a class="fn-backref" href="#id5">2</a>, <a class="fn-backref" href="#id6">3</a>)</em> Force constant internally divided by 2.0</td></tr>
</tbody>
</table>
</div>
<div class="section" id="dihedraltypes">
<h3>[ dihedraltypes ]<a class="headerlink" href="#dihedraltypes" title="Permalink to this headline">¶</a></h3>
<table border="1" class="docutils">
<colgroup>
<col width="43%" />
<col width="9%" />
<col width="48%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Name of interaction</th>
<th class="head">func</th>
<th class="head">params</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>HarmonicNCos <a class="reference internal" href="#eq4">eq4</a></td>
<td>1</td>
<td>phi0 (deg), K, multiplicity</td>
</tr>
<tr class="row-odd"><td>Ryckaert Bellemans <a class="reference internal" href="#eq5">eq5</a></td>
<td>3</td>
<td>K0, K1, K2, K3, K4, K5</td>
</tr>
<tr class="row-even"><td>Tabulated</td>
<td>8</td>
<td>table index</td>
</tr>
<tr class="row-odd"><td>Harmonic <a class="reference internal" href="#eq7">eq7</a></td>
<td>12</td>
<td>phi0 (deg), K</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="nonbond-params">
<h3>[ nonbond_params ]<a class="headerlink" href="#nonbond-params" title="Permalink to this headline">¶</a></h3>
<p>Every line should follow the format</p>
<div class="highlight-none"><div class="highlight"><pre><span></span>T1 T2 func <params>
</pre></div>
</div>
<p>where <cite>T1</cite>, <cite>T2</cite> are atom types, <cite>func</cite> defines the type of non-bonded
interaction and <cite>params</cite> is the set of parameters.
We show the list of currently available non-bonded interactions with the corresponding
parameters in the table below.</p>
<table border="1" class="docutils">
<colgroup>
<col width="27%" />
<col width="3%" />
<col width="71%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Name of interaction</th>
<th class="head">func</th>
<th class="head">params</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Lennard-Jones <a class="reference internal" href="#lj">lj</a></td>
<td>1</td>
<td>sigma <a class="footnote-reference" href="#f1" id="id8">[3]</a>, epsilon <a class="footnote-reference" href="#f1" id="id9">[3]</a></td>
</tr>
<tr class="row-odd"><td>Tabulated</td>
<td>8</td>
<td>filename <a class="footnote-reference" href="#f2" id="id10">[4]</a></td>
</tr>
<tr class="row-even"><td>Tabulated (conversion) <a class="reference internal" href="#tc">tc</a></td>
<td>9</td>
<td>filename*, type, total number, p_min, p_max, is_default*</td>
</tr>
<tr class="row-odd"><td>Tabulated (mixed, conversion)</td>
<td>10</td>
<td>tab1, tab2, type, total_number</td>
</tr>
<tr class="row-even"><td>Tabulated scaled by lambda</td>
<td>11</td>
<td>filename*, max_force*</td>
</tr>
<tr class="row-odd"><td>Tabulated (mixed, static)</td>
<td>12</td>
<td>tab1, tab2, mix value</td>
</tr>
<tr class="row-even"><td>Tabulated (cap radius)</td>
<td>13</td>
<td>filename, cap radius</td>
</tr>
<tr class="row-odd"><td>Tabulated (scaled pairs)</td>
<td>14</td>
<td>filename, scale increment, max_force*</td>
</tr>
<tr class="row-even"><td>Lennard-Jones scaled by lambda</td>
<td>15</td>
<td>sigma*, epsilon*, max_force*</td>
</tr>
<tr class="row-odd"><td>Lennard-Jones capped</td>
<td>16</td>
<td>sigma*, epsilon*, cap radius</td>
</tr>
<tr class="row-even"><td>Tabulated (multi mixed)</td>
<td>17</td>
<td>type, total number, p_min:p_max:table1:table2, p_min:p_max:table1:table2, p_min:p_max:table1:table2, …</td>
</tr>
<tr class="row-odd"><td>Tabulated (scaled pairs from file) <a href="#id11"><span class="problematic" id="id12">ts_</span></a></td>
<td>18</td>
<td>tab filename, pair list filename, scaling factor (default: 0.0)</td>
</tr>
</tbody>
</table>
<p class="rubric">Footnotes</p>
<table class="docutils footnote" frame="void" id="f1" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label">[3]</td><td><em>(<a class="fn-backref" href="#id8">1</a>, <a class="fn-backref" href="#id9">2</a>)</em> If not set then the values are taken from the included force-field.</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="f2" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id10">[4]</a></td><td>if the filename is not given then it will be constructed from atom type names: ‘table_T1_T2.xvg’ where T1, T2 are</td></tr>
</tbody>
</table>
<p>type names.</p>
</div>
</div>
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