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<span class="sd">.. footbibliography::</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">MDAnalysis.lib.correlations</span> <span class="kn">import</span> <span class="n">autocorrelation</span><span class="p">,</span> <span class="n">correct_intermittency</span>
<span class="kn">import</span> <span class="nn">MDAnalysis.analysis.hbonds</span>
<span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">zip_longest</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">import</span> <span class="nn">warnings</span>
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<p>where <span class="math notranslate nohighlight">\(\tau\)</span> is the timestep, <span class="math notranslate nohighlight">\(N(t)\)</span> the number of particles at time
<span class="math notranslate nohighlight">\(t\)</span>, and <span class="math notranslate nohighlight">\(N(t, t+\tau)\)</span> is the number of particles at every frame from
<span class="math notranslate nohighlight">\(t\)</span> to <span class="math notranslate nohighlight">\(t + \tau\)</span>. The angular brackets represent an average over all time
origins, <span class="math notranslate nohighlight">\(t\)</span>. See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/lib/correlations.html#MDAnalysis.lib.correlations.autocorrelation" title="(in MDAnalysis v2.6.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.correlations.autocorrelation()</span></code></a> for
origins, <span class="math notranslate nohighlight">\(t\)</span>. See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/lib/correlations.html#MDAnalysis.lib.correlations.autocorrelation" title="(in MDAnalysis v2.7.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.correlations.autocorrelation()</span></code></a> for
technical details.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<section id="hydrogenbondlifetimes">
<h2>HydrogenBondLifetimes<a class="headerlink" href="#hydrogenbondlifetimes" title="Link to this heading"></a></h2>
<p>To analyze hydrogen bond lifetime, use
<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/hydrogenbonds.html#MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime" title="(in MDAnalysis v2.6.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime()</span></code></a>.</p>
<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/hydrogenbonds.html#MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime" title="(in MDAnalysis v2.7.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime()</span></code></a>.</p>
<div class="admonition seealso">
<p class="admonition-title">See also</p>
<p><a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/hydrogenbonds.html#module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis" title="(in MDAnalysis v2.6.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.hydrogenbonds.hbond_analysis</span></code></a></p>
<p><a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/hydrogenbonds.html#module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis" title="(in MDAnalysis v2.7.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.hydrogenbonds.hbond_analysis</span></code></a></p>
</div>
</section>
<section id="waterorientationalrelaxation">
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</ul>
<p class="rubric">References</p>
<div class="docutils container" id="id8">
<aside class="footnote brackets" id="footcite-yeh1999" role="note">
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<aside class="footnote brackets" id="footcite-yeh1999" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
<p>Yu-ling Yeh and Chung-Yuan Mou. Orientational relaxation dynamics of liquid water studied by molecular dynamics simulation. <em>The Journal of Physical Chemistry B</em>, 103(18):3699–3705, 1999. <a class="reference external" href="https://doi.org/10.1021/jp984584r">doi:10.1021/jp984584r</a>.</p>
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<aside class="footnote brackets" id="footcite-rapaport1983" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id2">2</a><span class="fn-bracket">]</span></span>
<p>D.C. Rapaport. Hydrogen bonds in water. <em>Molecular Physics</em>, 50(5):1151–1162, 1983. <a class="reference external" href="https://doi.org/10.1080/00268978300102931">doi:10.1080/00268978300102931</a>.</p>
</aside>
<aside class="footnote brackets" id="footcite-grigera1995" role="note">
<aside class="footnote brackets" id="footcite-grigera1995" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id3">3</a><span class="fn-bracket">]</span></span>
<p>J. Raul Grigera, Susana G. Kalko, and Jorge Fischbarg. Wall−water interface. a molecular dynamics study. <em>Langmuir</em>, 12(1):154–158, 1996. <a class="reference external" href="https://doi.org/10.1021/la9408681">doi:10.1021/la9408681</a>.</p>
</aside>
<aside class="footnote brackets" id="footcite-brodka1994" role="note">
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<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id4">4</a><span class="fn-bracket">]</span></span>
<p>Aleksander Bródka. Diffusion in restricted volume. <em>Molecular Physics</em>, 82(5):1075–1078, 1994. <a class="reference external" href="https://doi.org/10.1080/00268979400100764">doi:10.1080/00268979400100764</a>.</p>
</aside>
<aside class="footnote brackets" id="footcite-liu2004" role="note">
<aside class="footnote brackets" id="footcite-liu2004" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id5">5</a><span class="fn-bracket">]</span></span>
<p>Pu Liu, Edward Harder, and B. J. Berne. On the calculation of diffusion coefficients in confined fluids and interfaces with an application to the liquid−vapor interface of water. <em>The Journal of Physical Chemistry B</em>, 108(21):6595–6602, 2004. <a class="reference external" href="https://doi.org/10.1021/jp0375057">doi:10.1021/jp0375057</a>.</p>
</aside>
<aside class="footnote brackets" id="footcite-arayasecchi2014" role="note">
<aside class="footnote brackets" id="footcite-arayasecchi2014" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id6">6</a><span class="fn-bracket">]</span></span>
<p>Raul Araya-Secchi, Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, Yerko Escalona, Jose-Antonio Garate, Agustin D. Martínez, Isaac E. García, Juan C. Sáez, and Ruhong Zhou. Characterization of a novel water pocket inside the human cx26 hemichannel structure. <em>Biophysical Journal</em>, 107(3):599–612, 2014. <a class="reference external" href="https://doi.org/10.1016/j.bpj.2014.05.037">doi:10.1016/j.bpj.2014.05.037</a>.</p>
</aside>
<aside class="footnote brackets" id="footcite-milischuk2011" role="note">
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<p>Anatoli A. Milischuk and Branka M. Ladanyi. Structure and dynamics of water confined in silica nanopores. <em>The Journal of Chemical Physics</em>, 135(17):174709, 2011. <a class="reference external" href="https://doi.org/10.1063/1.3657408">doi:10.1063/1.3657408</a>.</p>
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