Fix/colbuilder tut (#394)

* move files and make file naming more consistent

* add genion prompt answer

* improve kimmdy run setup section

* add sentence about checkpoints

* refactor plumed file

* chore(docs): render docs

---------

Co-authored-by: Eric Hartmann <hartmaec@rh05659.villa-bosch.de>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

docs/guide/explanation/index.html

@@ -537,7 +537,7 @@ <h1 class="title">Explanations</h1>
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 <td>
 <a href="../../guide/explanation/topology.html" class="title listing-title">Visualize Topologies</a>
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docs/guide/how-to/index.html

@@ -537,39 +537,39 @@ <h1 class="title">How-To</h1>
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+<tr data-index="0" data-listing-file-modified-sort="1709129553918" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
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-<tr data-index="1" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
+<tr data-index="1" data-listing-file-modified-sort="1709129553918" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
 <td>
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 </td>
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-<tr data-index="2" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
+<tr data-index="2" data-listing-file-modified-sort="1709129553918" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
 <td>
 <a href="../../guide/how-to/hcp.html" class="title listing-title">High Performance Computing</a>
 </td>
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 <span class="listing-author">&nbsp;</span>
 </td>
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-<tr data-index="3" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
+<tr data-index="3" data-listing-file-modified-sort="1709129553918" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
 <td>
 <a href="../../guide/how-to/install-ml-plugins.html" class="title listing-title">Install Machine Learning Plugins</a>
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 <td>
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 </tr>
-<tr data-index="4" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
+<tr data-index="4" data-listing-file-modified-sort="1709129553918" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
 <td>
 <a href="../../guide/how-to/reaction_only.html" class="title listing-title">Reaction only</a>
 </td>

docs/guide/tutorials/getting-started.html

@@ -603,7 +603,7 @@ <h2 class="anchored" data-anchor-id="setup-the-simulation">Setup the Simulation<
 <p>Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin <code>hat_reaction</code> to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.</p>
     <div id="app-./getting-started-files/vis-ala.molj" class="molstar-app"></div>
     <script type="text/javascript">
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+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"viewportShowExpand":true,"layoutShowControls":false,"layoutShowLog":false,"layoutShowLeftPanel":true,"emdbProvider":"rcsb","pdbProvider":"rcsb","layoutShowSequence":false,"viewportShowAnimation":true,"layoutIsExpanded":false,"viewportShowSelectionMode":false,"layoutShowRemoteState":false}).then(viewer => {
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docs/guide/tutorials/index.html

@@ -507,7 +507,7 @@ <h1 class="title">Tutorials</h1>
 
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-<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="3">
+<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1709129553922" data-listing-reading-time-sort="3">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/getting-started.html"> <img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"> </a></p>
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@@ -539,7 +539,7 @@ <h3 class="no-anchor listing-title">
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 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709129553918" data-listing-reading-time-sort="6">
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 <p><a href="../../guide/tutorials/colbuilder.html"> <img src="../../guide/tutorials/img/colbuilder.png" class="thumbnail-image"> </a></p>
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@@ -571,7 +571,7 @@ <h3 class="no-anchor listing-title">
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-<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709062041710" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709129553926" data-listing-reading-time-sort="6">
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 <p><a href="../../guide/tutorials/write-plugin.html"> <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div> </a></p>
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