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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
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<link href="index_files/libs/quarto-contrib/molstar-v3.13.0/app-container.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.4.554">
<meta name="author" content="Jannik Buhr, MBM">
<meta name="dcterms.date" content="2024-06-03">
<title>KIMMDY Reactive Molecular Dynamics using Kinetic Monte Carlo</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
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<div class="slides">
<section id="title-slide" data-background-color="white" data-background-image="./www/helix-wide.png" data-background-position="center bottom -10%" data-background-size="contain" class="quarto-title-block center">
<h1 class="title"><p><strong>KIMMDY</strong><br>
Reactive Molecular Dynamics<br>
using<br>
Kinetic Monte Carlo</p></h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Jannik Buhr, MBM
</div>
<p class="quarto-title-affiliation">
Heidelberg Institute for Theoretical Studies
</p>
</div>
</div>
<p class="date">June 3, 2024</p>
</section>
<section id="collagen-has-interesting-chemistry-under-mechanical-stress" class="slide level2" data-background-image="./img/collagen.png" data-background-color="black">
<h2>Collagen has interesting chemistry under mechanical stress</h2>
</section>
<section id="how-do-we-simulating-large-molecular-systems" class="slide level2">
<h2>How do we simulating (large) molecular systems?</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><img data-src="img/monkey.png" class="img-fluid" style="width:90.0%"></p>
</div><div class="column" style="width:50%;">
<h3 id="bonds-do-not-exist.">Bonds do not exist.</h3>
<div class="r-stack center">
<p><img data-src="./img/molecule-vdw.png" class="img-fluid"></p>
<p><img data-src="./img/molecule-density.png" class="fragment img-fluid"></p>
<p><img data-src="./img/molecule-cpk.png" class="fragment img-fluid"></p>
</div>
<h3 class="fragment" id="but-lets-pretend-they-do.">But let’s pretend they do.</h3>
</div>
</div>
</section>
<section id="molecular-dynamics-molecular-mechanics-newton-to-the-rescue" class="slide level2">
<h2>Molecular Dynamics / Molecular Mechanics – Newton to the rescue!</h2>
<div class="columns">
<div class="column" style="width:40%;">
<p><span class="math display">\[E_{total} = E_{bonded} + E_{nonbonded}\]</span> <span class="math display">\[E_{bonded}=E_{\text{bond}}+E_{\text{angle}}+E_{\text{dihedral}}\]</span> <span class="math display">\[E_{nonbonded} = E_{\text{electrostatic}} + E_{\text{van der Waals}}\]</span></p>
</div><div class="column" style="width:30%;">
<p><img data-src="./img/molecule-cpk.png" id="mol1" class="img-fluid"></p>
</div><div class="column" style="width:30%;">
<p><img data-src="./img/molecule-cpk.png" id="mol2" class="img-fluid"></p>
</div>
</div>
<h3 class="fragment" id="popular-potential-energy-functions">Popular Potential Energy Functions</h3>
<hr>
<div class="columns">
<div class="column fragment" style="width:30%;">
<div id="oh">
<p><img data-src="./img/hyd-oh.png" class="img-fluid"></p>
</div>
<div id="26830b12" class="cell" data-execution_count="2">
<div class="cell-output cell-output-display">
<div>
<figure>
<p><img data-src="index_files/figure-revealjs/cell-3-output-1.png" class="img-fluid"></p>
</figure>
</div>
</div>
</div>
<p><span class="math display">\[E_{morse}(r) = D \left(1 - e^{-\beta(r - r_0)}\right)^2\]</span></p>
</div><div class="column fragment" style="width:30%;">
<div id="water">
<p><img data-src="./img/water.png" class="img-fluid"></p>
</div>
<div id="26746ac3" class="cell" data-execution_count="3">
<div class="cell-output cell-output-display">
<div>
<figure>
<p><img data-src="index_files/figure-revealjs/cell-4-output-1.png" class="img-fluid"></p>
</figure>
</div>
</div>
</div>
<p><span class="math display">\[E_{harmonic}(r) = \frac{1}{2} k (r - r_0)^2\]</span></p>
</div><div class="column fragment" style="width:30%;">
<div id="3ce1a0a2" class="cell" data-execution_count="4">
<div class="cell-output cell-output-display">
<div>
<figure>
<p><img data-src="index_files/figure-revealjs/cell-5-output-1.png" class="img-fluid"></p>
</figure>
</div>
</div>
</div>
<p><span class="math display">\[E_{cosine}(\phi) = k_\phi (1 + \cos(n \phi - \phi_0))\]</span></p>
</div>
</div>
<div id="meme-harmonic" class="fragment">
<p><img data-src="img/meme-harmonic.png" class="img-fluid" style="width:85.0%"></p>
</div>
</section>
<section id="force-fields-list-the-parameters-for-these-potentials" class="slide level2">
<h2>Force Fields list the parameters for these potentials</h2>
<p>e.g. AMBER99SB*-ILDNP <span class="citation" data-cites="cornellSecondGenerationForce1995 alievMotionalTimescalePredictions2014">(<a href="#/references" role="doc-biblioref" onclick="">Cornell et al. 1995</a>; <a href="#/references" role="doc-biblioref" onclick="">Aliev et al. 2014</a>)</span></p>
<div class="columns">
<div class="column" style="width:40%;">
<div class="code-with-filename">
<div class="code-with-filename-file">
<pre><strong>forcefield.itp</strong></pre>
</div>
<pre class="itp" data-filename="forcefield.itp"><code>#include "ffnonbonded.itp"
#include "ffbonded.itp"</code></pre>
</div>
<div class="code-with-filename">
<div class="code-with-filename-file">
<pre><strong>ffnonbonded.itp</strong></pre>
</div>
<pre class="itp" data-filename="ffnonbonded.itp"><code>[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01</code></pre>
</div>
<div class="code-with-filename">
<div class="code-with-filename-file">
<pre><strong>ffbonded.itp</strong></pre>
</div>
<pre class="itp" data-filename="ffbonded.itp"><code>[ bondtypes ]
; i j func b0 kb
C C 1 0.1525 259408.0
C OS 1 0.1323 376560.0
[ angletypes ]
...</code></pre>
</div>
<div id="harmonic">
<p><span class="math display">\[V_{harmonic}(r) = \frac{1}{2} k (r - r_0)^2\]</span></p>
</div>
</div><div class="column" style="width:50%;">
<p><img data-src="./img/molecule-cpk.png" class="img-fluid"></p>
</div>
</div>
<h3 class="fragment cent" id="but-what-about-chemistry">But what about Chemistry?</h3>
</section>
<section id="welcome-to-kimmdy" class="slide level2">
<h2>Welcome to KIMMDY!</h2>
<p><em>Project with Kai Riedmiller and Eric Hartmann</em></p>
<p><a href="https://hits-mbm-dev.github.io/kimmdy/" class="uri">https://hits-mbm-dev.github.io/kimmdy/</a></p>
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<p><img data-src="./img/ala-rad.png" id="ala-rad" class="img-fluid"></p>
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<div class="columns">
<div class="column" style="width:20%;">
<div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install kimmdy</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="" aria-hidden="true" tabindex="-1"></a><span class="ex">edit</span> kimmdy.yml</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<span id="cb6-2"><a href="" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> equilibrium</span></span>
<span id="cb6-3"><a href="" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> </span><span class="fu">mult</span><span class="kw">:</span><span class="at"> </span><span class="dv">4</span></span>
<span id="cb6-4"><a href="" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="fu">tasks</span><span class="kw">:</span></span>
<span id="cb6-5"><a href="" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> reactions</span></span>
<span id="cb6-6"><a href="" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> equilibrium</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<h2>KIMMDY is user-friendly</h2>
<div class="columns">
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<h2>KIMMDY is extensible</h2>
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<ul>
<li>Simple python plugin</li>
<li>Take <strong>state</strong> of the system</li>
<li>Return <strong>rates</strong> and <strong>recipes</strong></li>
<li>KIMMDY takes care of topology details</li>
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<h3 id="example-peptide-bond-hydrolysis">Example: Peptide bond hydrolysis</h3>
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<section>
<section id="thank-you" class="title-slide slide level1 center">
<h1>Thank You!</h1>
<div id="otter">
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</section>
<section id="thank-you-1" class="slide level2">
<h2>Thank You!</h2>
<div id="mbm-group">
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<div id="bar">
<div class="profile">
<ul>
<li><a href="https://mbm.h-its.org" class="bi-house">mbm.h-its.org</a></li>
<li><a href="hhttps://github.com/hits-mbm-dev" class="bi-github">hits-mbm-dev</a></li>
<li><a href="https://github.com/jmbuhr" class="bi-github">jmbuhr</a></li>
<li><a href="https://jmbuhr.de" class="bi-house">jmbuhr.de</a></li>
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<div id="acknowledge">
<p>This work was supported by the Klaus Tschira Foundation and has received funding from the European Research Council (ERC)</p>
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<section id="references" class="slide level2 smaller scrollable">
<h2>References</h2>
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<div id="ref-alievMotionalTimescalePredictions2014" class="csl-entry" role="listitem">
Aliev, Abil E, Martin Kulke, Harmeet S Khaneja, Vijay Chudasama, Tom D Sheppard, and Rachel M Lanigan. 2014. <span>“Motional Timescale Predictions by Molecular Dynamics Simulations: Case Study Using Proline and Hydroxyproline Sidechain Dynamics.”</span> <a href="https://doi.org/10.1002/prot.24350">https://doi.org/10.1002/prot.24350</a>.
</div>
<div id="ref-allaireQuarto2022c" class="csl-entry" role="listitem">
Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2022. <span>“Quarto.”</span> <a href="https://github.com/quarto-dev/quarto-cli">https://github.com/quarto-dev/quarto-cli</a>.
</div>
<div id="ref-cornellSecondGenerationForce1995" class="csl-entry" role="listitem">
Cornell, Wendy D., Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman. 1995. <span>“A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules.”</span> <a href="https://doi.org/10.1021/ja00124a002">https://doi.org/10.1021/ja00124a002</a>.
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