diff --git a/biobb_wf_ligand_parameterization/html/biobb_wf_ligand_parameterization.web.html b/biobb_wf_ligand_parameterization/html/biobb_wf_ligand_parameterization.web.html
index 6d7200a..31fff64 100644
--- a/biobb_wf_ligand_parameterization/html/biobb_wf_ligand_parameterization.web.html
+++ b/biobb_wf_ligand_parameterization/html/biobb_wf_ligand_parameterization.web.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head><meta charset="utf-8"/>
 <meta content="width=device-width, initial-scale=1.0" name="viewport"/>
-<title>biobb_wf_ligand_parameterization.web</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
+<title>biobb_MDsetup_tutorial.web</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
 <style type="text/css">
     pre { line-height: 125%; }
 td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
@@ -7516,38 +7516,47 @@
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="Automatic-Ligand-parameterization-tutorial-using-BioExcel-Building-Blocks-(biobb)">Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)<a class="anchor-link" href="#Automatic-Ligand-parameterization-tutorial-using-BioExcel-Building-Blocks-(biobb)">¶</a></h1><hr/>
-<p>This tutorial aims to illustrate the process of <strong>ligand parameterization</strong> for a <strong>small molecule</strong>, step by step, using the <strong>BioExcel Building Blocks library (biobb)</strong>. The particular example used is the <strong>Ibuprofen</strong> small compound (3-letter code IBP, Drugbank code <a href="https://www.drugbank.ca/drugs/DB01050">DB01050</a>), a non-steroidal <strong>anti-inflammatory drug</strong> (NSAID) derived from propionic acid and it is considered the first of the propionics.</p>
-<p><strong>OpenBabel and ACPype</strong> packages are used to <strong>add hydrogens</strong>, <strong>energetically minimize the structure</strong>, and
-<strong>generate parameters</strong> for the <strong>GROMACS</strong> package. With <em>Generalized Amber Force Field (GAFF)</em> forcefield and <em>AM1-BCC</em> charges.</p>
+<h1 id="Protein-MD-Setup-tutorial-using-BioExcel-Building-Blocks-(biobb)">Protein MD Setup tutorial using BioExcel Building Blocks (biobb)<a class="anchor-link" href="#Protein-MD-Setup-tutorial-using-BioExcel-Building-Blocks-(biobb)">¶</a></h1><p><strong>Based on the official GROMACS tutorial:</strong> <a href="http://www.mdtutorials.com/gmx/lysozyme/index.html">http://www.mdtutorials.com/gmx/lysozyme/index.html</a></p>
 <hr/>
-<p><strong>Biobb modules</strong> used:</p>
-<ul>
-<li><a href="https://github.com/bioexcel/biobb_io">biobb_io</a>: Tools to fetch data to be consumed by the rest of the Biobb building blocks.</li>
-<li><a href="https://github.com/bioexcel/biobb_chemistry">biobb_chemistry</a>: Tools to manipulate chemistry data.</li>
+<p>This tutorial aims to illustrate the process of <strong>setting up a simulation system</strong> containing a <strong>protein</strong>, step by step, using the <strong>BioExcel Building Blocks library (biobb)</strong>. The particular example used is the <strong>Lysozyme</strong> protein (PDB code 1AKI, <a href="https://doi.org/10.2210/pdb1AKI/pdb">https://doi.org/10.2210/pdb1AKI/pdb</a>).</p>
+<hr/>
+<h2 id="Settings">Settings<a class="anchor-link" href="#Settings">¶</a></h2><h3 id="Biobb-modules-used">Biobb modules used<a class="anchor-link" href="#Biobb-modules-used">¶</a></h3><ul>
+<li><a href="https://github.com/bioexcel/biobb_io">biobb_io</a>: Tools to fetch biomolecular data from public databases.</li>
+<li><a href="https://github.com/bioexcel/biobb_model">biobb_model</a>: Tools to model macromolecular structures.</li>
+<li><a href="https://github.com/bioexcel/biobb_gromacs">biobb_gromacs</a>: Tools to setup and run Molecular Dynamics simulations.</li>
+<li><a href="https://github.com/bioexcel/biobb_analysis">biobb_analysis</a>: Tools to analyse Molecular Dynamics trajectories.</li>
 </ul>
 <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link" href="#Auxiliary-libraries-used">¶</a></h3><ul>
 <li><a href="https://jupyter.org/">jupyter</a>: Free software, open standards, and web services for interactive computing across all programming languages.</li>
 <li><a href="http://nglviewer.org/#nglview">nglview</a>: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.</li>
+<li><a href="https://plot.ly/python/offline/">plotly</a>: Python interactive graphing library integrated in Jupyter notebooks.</li>
+<li><a href="https://github.com/arose/simpletraj">simpletraj</a>: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.</li>
 </ul>
-<h3 id="Conda-Installation-and-Launch">Conda Installation and Launch<a class="anchor-link" href="#Conda-Installation-and-Launch">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_ligand_parameterization.git</span>
-<span class="go">cd biobb_wf_ligand_parameterization</span>
+<h3 id="Conda-Installation-and-Launch">Conda Installation and Launch<a class="anchor-link" href="#Conda-Installation-and-Launch">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_md_setup.git</span>
+<span class="go">cd biobb_wf_md_setup</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_wf_ligand_parameterization</span>
-<span class="go">jupyter-notebook biobb_wf_ligand_parameterization/notebooks/biobb_wf_ligand_parameterization.ipynb</span>
+<span class="go">conda activate biobb_wf_md_setup</span>
+<span class="go">jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb</span>
 </pre></div>
 <hr/>
-<h3 id="Pipeline-steps:">Pipeline steps:<a class="anchor-link" href="#Pipeline-steps:">¶</a></h3><ol>
+<h2 id="Pipeline-steps">Pipeline steps<a class="anchor-link" href="#Pipeline-steps">¶</a></h2><ol>
 <li><a href="#input">Input Parameters</a></li>
-<li><a href="#fetch">Fetching Ligand Structure</a></li>
-<li><a href="#addh">Add Hydrogen Atoms</a></li>
-<li><a href="#min">Energetically Minimize Hydrogen Atoms</a></li>
-<li><a href="#acpype">Generating Ligand Parameters</a></li>
+<li><a href="#fetch">Fetching PDB Structure</a></li>
+<li><a href="#fix">Fix Protein Structure</a></li>
+<li><a href="#top">Create Protein System Topology</a></li>
+<li><a href="#box">Create Solvent Box</a></li>
+<li><a href="#water">Fill the Box with Water Molecules</a></li>
+<li><a href="#ions">Adding Ions</a></li>
+<li><a href="#min">Energetically Minimize the System</a></li>
+<li><a href="#nvt">Equilibrate the System (NVT)</a></li>
+<li><a href="#npt">Equilibrate the System (NPT)</a></li>
+<li><a href="#free">Free Molecular Dynamics Simulation</a></li>
+<li><a href="#post">Post-processing and Visualizing Resulting 3D Trajectory</a></li>
 <li><a href="#output">Output Files</a></li>
 <li><a href="#questions">Questions &amp; Comments</a></li>
 </ol>
 <hr/>
-<p><img alt="" src="https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png"/></p>
+<p><img alt="Bioexcel2 logo" src="https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png" title="Bioexcel2 logo" width="400"/></p>
 <hr/>
 </div>
 </div>
@@ -7568,7 +7577,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
 <div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Only executed when using google colab</span>
@@ -7583,7 +7592,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
     <span class="kn">import</span> <span class="nn">condacolab</span>
     <span class="n">condacolab</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
     <span class="c1"># Clone repository</span>
-    <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_ligand_parameterization.git"</span>
+    <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_md_setup.git"</span>
     <span class="n">repo_name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_URL</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_name</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
       <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"mamba"</span><span class="p">,</span> <span class="s2">"install"</span><span class="p">,</span> <span class="s2">"-y"</span><span class="p">,</span> <span class="s2">"git"</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
@@ -7606,7 +7615,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
 <div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Enable widgets for colab</span>
@@ -7615,7 +7624,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
   <span class="n">output</span><span class="o">.</span><span class="n">enable_custom_widget_manager</span><span class="p">()</span>
   <span class="c1"># Change working dir</span>
   <span class="kn">import</span> <span class="nn">os</span>
-  <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_ligand_parameterization/biobb_wf_ligand_parameterization/notebooks"</span><span class="p">)</span>
+  <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_md_setup/biobb_wf_md_setup/notebooks"</span><span class="p">)</span>
   <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"📂 New working directory: </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -7630,12 +7639,9 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
 <p><a id="input"></a></p>
-<hr/>
 <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-parameters">¶</a></h2><p><strong>Input parameters</strong> needed:</p>
 <ul>
-<li><strong>ligandCode</strong>: 3-letter code of the ligand structure (e.g. IBP, Drugbank code <a href="https://www.drugbank.ca/drugs/DB01050">DB01050</a>)</li>
-<li><strong>mol_charge</strong>: Molecule net charge (e.g. -1)</li>
-<li><strong>pH</strong>: Acidity or alkalinity for the small molecule. Hydrogen atoms will be added according to this pH. (e.g. 7.4)</li>
+<li><strong>pdbCode</strong>: PDB code of the protein structure (e.g. 1AKI, <a href="https://doi.org/10.2210/pdb1AKI/pdb">https://doi.org/10.2210/pdb1AKI/pdb</a>)</li>
 </ul>
 </div>
 </div>
@@ -7645,16 +7651,13 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
 <div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">nglview</span>
 <span class="kn">import</span> <span class="nn">ipywidgets</span>
-<span class="kn">import</span> <span class="nn">os</span>
 
-<span class="n">ligandCode</span> <span class="o">=</span> <span class="s1">'IBP'</span>
-<span class="n">mol_charge</span> <span class="o">=</span> <span class="mi">-1</span>
-<span class="n">pH</span> <span class="o">=</span> <span class="mf">7.4</span>
+<span class="n">pdbCode</span> <span class="o">=</span> <span class="s2">"1AKI"</span>
 </pre></div>
 </div>
 </div>
@@ -7669,12 +7672,12 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
 <p><a id="fetch"></a></p>
 <hr/>
-<h2 id="Fetching-ligand-structure">Fetching ligand structure<a class="anchor-link" href="#Fetching-ligand-structure">¶</a></h2><p>Downloading <strong>ligand structure</strong> in <strong>PDB format</strong> from the IRB PDB MIRROR database.<br/>
+<h2 id="Fetching-PDB-structure">Fetching PDB structure<a class="anchor-link" href="#Fetching-PDB-structure">¶</a></h2><p>Downloading <strong>PDB structure</strong> with the <strong>protein molecule</strong> from the RCSB PDB database.<br/>
 Alternatively, a <strong>PDB file</strong> can be used as starting structure. <br/></p>
 <hr/>
 <p><strong>Building Blocks</strong> used:</p>
 <ul>
-<li><a href="https://biobb-io.readthedocs.io/en/latest/api.html#module-api.ligand">Ligand</a> from <strong>biobb_io.api.ligand</strong></li>
+<li><a href="https://biobb-io.readthedocs.io/en/latest/api.html#module-api.pdb">Pdb</a> from <strong>biobb_io.api.pdb</strong></li>
 </ul>
 <hr/>
 </div>
@@ -7685,23 +7688,22 @@ <h2 id="Fetching-ligand-structure">Fetching ligand structure<a class="anchor-lin
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Ligand: Download ligand structure from MMB PDB mirror REST API (https://mmb.irbbarcelona.org/api/)</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Downloading desired PDB file </span>
 <span class="c1"># Import module</span>
-<span class="kn">from</span> <span class="nn">biobb_io.api.ligand</span> <span class="kn">import</span> <span class="n">ligand</span>
-
-<span class="c1"># Create prop dict and inputs/outputs</span>
-<span class="n">input_structure</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'.pdb'</span>
+<span class="kn">from</span> <span class="nn">biobb_io.api.pdb</span> <span class="kn">import</span> <span class="n">pdb</span>
 
+<span class="c1"># Create properties dict and inputs/outputs</span>
+<span class="n">downloaded_pdb</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'.pdb'</span>
 <span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
-    <span class="s1">'ligand_code'</span> <span class="p">:</span> <span class="n">ligandCode</span>
+    <span class="s1">'pdb_code'</span><span class="p">:</span> <span class="n">pdbCode</span>
 <span class="p">}</span>
 
 <span class="c1">#Create and launch bb</span>
-<span class="n">ligand</span><span class="p">(</span><span class="n">output_pdb_path</span><span class="o">=</span><span class="n">input_structure</span><span class="p">,</span>
-        <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+<span class="n">pdb</span><span class="p">(</span><span class="n">output_pdb_path</span><span class="o">=</span><span class="n">downloaded_pdb</span><span class="p">,</span>
+    <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -7714,7 +7716,8 @@ <h2 id="Fetching-ligand-structure">Fetching ligand structure<a class="anchor-lin
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the downloaded/given <strong>ligand PDB structure</strong> using <strong>NGL</strong>:</p>
+<p><a id="vis3D"></a></p>
+<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the downloaded/given <strong>PDB structure</strong> using <strong>NGL</strong>:</p>
 </div>
 </div>
 </div>
@@ -7723,14 +7726,13 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1">#Show small ligand structure</span>
-<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">input_structure</span><span class="p">)</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Show protein</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">downloaded_pdb</span><span class="p">)</span>
 <span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'all'</span><span class="p">)</span>
-<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'300px'</span><span class="p">])</span>
-<span class="n">view</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
+<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'600px'</span><span class="p">])</span>
 <span class="n">view</span>
 </pre></div>
 </div>
@@ -7744,7 +7746,7 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><img src='ngl1.png' id="64871a1c9b6a62.34741727" data-width="500" data-height="250"></img></p>
+<p><img src='ngl1.png' id="6488381a81fd32.60667683" data-width="600" data-height="450"></img></p>
 </div>
 </div>
 </div>
@@ -7755,13 +7757,17 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><a id="addh"></a></p>
+<p><a id="fix"></a></p>
 <hr/>
-<h2 id="Add-Hydrogen-Atoms">Add Hydrogen Atoms<a class="anchor-link" href="#Add-Hydrogen-Atoms">¶</a></h2><p>Adding <strong>Hydrogen atoms</strong> to the small molecule, according to the given pH.</p>
+<h2 id="Fix-protein-structure">Fix protein structure<a class="anchor-link" href="#Fix-protein-structure">¶</a></h2><p><strong>Checking</strong> and <strong>fixing</strong> (if needed) the protein structure:<br/></p>
+<ul>
+<li><strong>Modeling</strong> <strong>missing side-chain atoms</strong>, modifying incorrect <strong>amide assignments</strong>, choosing <strong>alternative locations</strong>.<br/></li>
+<li><strong>Checking</strong> for missing <strong>backbone atoms</strong>, <strong>heteroatoms</strong>, <strong>modified residues</strong> and possible <strong>atomic clashes</strong>.</li>
+</ul>
 <hr/>
 <p><strong>Building Blocks</strong> used:</p>
 <ul>
-<li><a href="https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_add_hydrogens">BabelAddHydrogens</a> from <strong>biobb_chemistry.babelm.babel_add_hydrogens</strong></li>
+<li><a href="https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain">FixSideChain</a> from <strong>biobb_model.model.fix_side_chain</strong></li>
 </ul>
 <hr/>
 </div>
@@ -7772,26 +7778,115 @@ <h2 id="Add-Hydrogen-Atoms">Add Hydrogen Atoms<a class="anchor-link" href="#Add-
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Babel_add_hydrogens: add Hydrogen atoms to a small molecule</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Check &amp; Fix PDB</span>
 <span class="c1"># Import module</span>
-<span class="kn">from</span> <span class="nn">biobb_chemistry.babelm.babel_add_hydrogens</span> <span class="kn">import</span> <span class="n">babel_add_hydrogens</span>
+<span class="kn">from</span> <span class="nn">biobb_model.model.fix_side_chain</span> <span class="kn">import</span> <span class="n">fix_side_chain</span>
 
 <span class="c1"># Create prop dict and inputs/outputs</span>
-<span class="n">output_babel_h</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'.H.mol2'</span> 
+<span class="n">fixed_pdb</span> <span class="o">=</span> <span class="n">pdbCode</span> <span class="o">+</span> <span class="s1">'_fixed.pdb'</span>
 
-<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
-    <span class="s1">'ph'</span> <span class="p">:</span> <span class="n">pH</span><span class="p">,</span>
-    <span class="s1">'input_format'</span> <span class="p">:</span> <span class="s1">'pdb'</span><span class="p">,</span>
-    <span class="s1">'output_format'</span> <span class="p">:</span> <span class="s1">'mol2'</span>
-<span class="p">}</span>
+<span class="c1"># Create and launch bb</span>
+<span class="n">fix_side_chain</span><span class="p">(</span><span class="n">input_pdb_path</span><span class="o">=</span><span class="n">downloaded_pdb</span><span class="p">,</span> 
+             <span class="n">output_pdb_path</span><span class="o">=</span><span class="n">fixed_pdb</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the fixed <strong>PDB structure</strong> using <strong>NGL</strong>. In this particular example, the checking step didn't find any issue to be solved, so there is no difference between the original structure and the fixed one.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Show protein</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">fixed_pdb</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'all'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'600px'</span><span class="p">])</span>
+<span class="n">view</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
+<span class="n">view</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><img src='ngl2.png' id="648838f702f712.02460877" data-width="600" data-height="450"></img></p>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="top"></a></p>
+<hr/>
+<h2 id="Create-protein-system-topology">Create protein system topology<a class="anchor-link" href="#Create-protein-system-topology">¶</a></h2><p><strong>Building GROMACS topology</strong> corresponding to the protein structure.<br/>
+Force field used in this tutorial is <a href="https://dx.doi.org/10.1002%2Fprot.22711"><strong>amber99sb-ildn</strong></a>: AMBER <strong>parm99</strong> force field with <strong>corrections on backbone</strong> (sb) and <strong>side-chain torsion potentials</strong> (ildn). Water molecules type used in this tutorial is <a href="https://pubs.acs.org/doi/abs/10.1021/j100308a038"><strong>spc/e</strong></a>.<br/>
+Adding <strong>hydrogen atoms</strong> if missing. Automatically identifying <strong>disulfide bridges</strong>. <br/></p>
+<p>Generating two output files:</p>
+<ul>
+<li><strong>GROMACS structure</strong> (gro file)</li>
+<li><strong>GROMACS topology</strong> ZIP compressed file containing:<ul>
+<li><em>GROMACS topology top file</em> (top file)</li>
+<li><em>GROMACS position restraint file/s</em> (itp file/s)</li>
+</ul>
+</li>
+</ul>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
+<ul>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.pdb2gmx">Pdb2gmx</a> from <strong>biobb_gromacs.gromacs.pdb2gmx</strong></li>
+</ul>
+<hr/>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Create system topology</span>
+<span class="c1"># Import module</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.pdb2gmx</span> <span class="kn">import</span> <span class="n">pdb2gmx</span>
 
-<span class="c1">#Create and launch bb</span>
-<span class="n">babel_add_hydrogens</span><span class="p">(</span><span class="n">input_path</span><span class="o">=</span><span class="n">input_structure</span><span class="p">,</span>
-                  <span class="n">output_path</span><span class="o">=</span><span class="n">output_babel_h</span><span class="p">,</span>
-                  <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+<span class="c1"># Create inputs/outputs</span>
+<span class="n">output_pdb2gmx_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_pdb2gmx.gro'</span>
+<span class="n">output_pdb2gmx_top_zip</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_pdb2gmx_top.zip'</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">pdb2gmx</span><span class="p">(</span><span class="n">input_pdb_path</span><span class="o">=</span><span class="n">fixed_pdb</span><span class="p">,</span> 
+        <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_pdb2gmx_gro</span><span class="p">,</span> 
+        <span class="n">output_top_zip_path</span><span class="o">=</span><span class="n">output_pdb2gmx_top_zip</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -7804,7 +7899,7 @@ <h2 id="Add-Hydrogen-Atoms">Add Hydrogen Atoms<a class="anchor-link" href="#Add-
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the <strong>ligand PDB structure</strong> with the newly added <strong>hydrogen atoms</strong> using <strong>NGL</strong>:</p>
+<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the generated <strong>GRO structure</strong> using <strong>NGL</strong>. Note that <strong>hydrogen atoms</strong> were added to the structure by the <strong>pdb2gmx GROMACS tool</strong> when generating the <strong>topology</strong>.</p>
 </div>
 </div>
 </div>
@@ -7813,12 +7908,13 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1">#Show small ligand structure</span>
-<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_babel_h</span><span class="p">)</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Show protein</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_pdb2gmx_gro</span><span class="p">)</span>
 <span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'all'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'600px'</span><span class="p">])</span>
 <span class="n">view</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
 <span class="n">view</span>
 </pre></div>
@@ -7833,7 +7929,7 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><img src='ngl2.png' id="64871cf88e90e0.84411521" data-width="500" data-height="250"></img></p>
+<p><img src='ngl3.png' id="64883a128d4954.88627566" data-width="600" data-height="450"></img></p>
 </div>
 </div>
 </div>
@@ -7844,13 +7940,14 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><a id="min"></a></p>
+<p><a id="box"></a></p>
 <hr/>
-<h2 id="Energetically-minimize-Hydrogen-Atoms">Energetically minimize Hydrogen Atoms<a class="anchor-link" href="#Energetically-minimize-Hydrogen-Atoms">¶</a></h2><p>Energetically minimize newly added <strong>Hydrogen atoms</strong>.</p>
+<h2 id="Create-solvent-box">Create solvent box<a class="anchor-link" href="#Create-solvent-box">¶</a></h2><p>Define the unit cell for the <strong>protein structure MD system</strong> to fill it with water molecules.<br/>
+A <strong>cubic box</strong> is used to define the unit cell, with a <strong>distance from the protein to the box edge of 1.0 nm</strong>. The protein is <strong>centered in the box</strong>.</p>
 <hr/>
 <p><strong>Building Blocks</strong> used:</p>
 <ul>
-<li><a href="https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_minimize">BabelMinimize</a> from <strong>biobb_chemistry.babelm.babel_minimize</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.editconf">Editconf</a> from <strong>biobb_gromacs.gromacs.editconf</strong></li>
 </ul>
 <hr/>
 </div>
@@ -7861,26 +7958,25 @@ <h2 id="Energetically-minimize-Hydrogen-Atoms">Energetically minimize Hydrogen A
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Babel_minimize: Structure energy minimization of a small molecule after being modified adding hydrogen atoms</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Editconf: Create solvent box</span>
 <span class="c1"># Import module</span>
-<span class="kn">from</span> <span class="nn">biobb_chemistry.babelm.babel_minimize</span> <span class="kn">import</span> <span class="n">babel_minimize</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.editconf</span> <span class="kn">import</span> <span class="n">editconf</span>
 
 <span class="c1"># Create prop dict and inputs/outputs</span>
-<span class="n">output_babel_min</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'.H.min.pdb'</span>                              
+<span class="n">output_editconf_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_editconf.gro'</span>
+
 <span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
-    <span class="s1">'method'</span> <span class="p">:</span> <span class="s1">'sd'</span><span class="p">,</span>
-    <span class="s1">'criteria'</span> <span class="p">:</span> <span class="s1">'1e-10'</span><span class="p">,</span>
-    <span class="s1">'force_field'</span> <span class="p">:</span> <span class="s1">'GAFF'</span>
+    <span class="s1">'box_type'</span><span class="p">:</span> <span class="s1">'cubic'</span><span class="p">,</span>
+    <span class="s1">'distance_to_molecule'</span><span class="p">:</span> <span class="mf">1.0</span>
 <span class="p">}</span>
 
-
 <span class="c1">#Create and launch bb</span>
-<span class="n">babel_minimize</span><span class="p">(</span><span class="n">input_path</span><span class="o">=</span><span class="n">output_babel_h</span><span class="p">,</span>
-              <span class="n">output_path</span><span class="o">=</span><span class="n">output_babel_min</span><span class="p">,</span>
-              <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+<span class="n">editconf</span><span class="p">(</span><span class="n">input_gro_path</span><span class="o">=</span><span class="n">output_pdb2gmx_gro</span><span class="p">,</span> 
+         <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_editconf_gro</span><span class="p">,</span>
+         <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -7893,7 +7989,16 @@ <h2 id="Energetically-minimize-Hydrogen-Atoms">Energetically minimize Hydrogen A
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the <strong>ligand PDB structure</strong> with the newly added <strong>hydrogen atoms</strong>, <strong>energetically minimized</strong>, using <strong>NGL</strong>:</p>
+<p><a id="water"></a></p>
+<hr/>
+<h2 id="Fill-the-box-with-water-molecules">Fill the box with water molecules<a class="anchor-link" href="#Fill-the-box-with-water-molecules">¶</a></h2><p>Fill the unit cell for the <strong>protein structure system</strong> with water molecules.<br/>
+The solvent type used is the default <strong>Simple Point Charge water (SPC)</strong>, a generic equilibrated 3-point solvent model.</p>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
+<ul>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.solvate">Solvate</a> from <strong>biobb_gromacs.gromacs.solvate</strong></li>
+</ul>
+<hr/>
 </div>
 </div>
 </div>
@@ -7902,13 +8007,51 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1">#Show small ligand structure</span>
-<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_babel_min</span><span class="p">)</span>
-<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'all'</span><span class="p">)</span>
-<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'300px'</span><span class="p">])</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Solvate: Fill the box with water molecules</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.solvate</span> <span class="kn">import</span> <span class="n">solvate</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_solvate_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_solvate.gro'</span>
+<span class="n">output_solvate_top_zip</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_solvate_top.zip'</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">solvate</span><span class="p">(</span><span class="n">input_solute_gro_path</span><span class="o">=</span><span class="n">output_editconf_gro</span><span class="p">,</span> 
+        <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_solvate_gro</span><span class="p">,</span> 
+        <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_pdb2gmx_top_zip</span><span class="p">,</span> 
+        <span class="n">output_top_zip_path</span><span class="o">=</span><span class="n">output_solvate_top_zip</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the <strong>protein system</strong> with the newly added <strong>solvent box</strong> using <strong>NGL</strong>.<br/> Note the <strong>cubic box</strong> filled with <strong>water molecules</strong> surrounding the <strong>protein structure</strong>, which is <strong>centered</strong> right in the middle of the cube.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Show protein</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_solvate_gro</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">clear_representations</span><span class="p">()</span>
+<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'cartoon'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'solute'</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">'green'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'SOL'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'600px'</span><span class="p">])</span>
 <span class="n">view</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
 <span class="n">view</span>
 </pre></div>
@@ -7923,7 +8066,7 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><img src='ngl3.png' id="64871d86eaa046.91556223" data-width="500" data-height="250"></img></p>
+<p><img src='ngl4.png' id="64883c2c40bcb6.14059733" data-width="600" data-height="450"></img></p>
 </div>
 </div>
 </div>
@@ -7934,12 +8077,112 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Visualizing-3D-structures">Visualizing 3D structures<a class="anchor-link" href="#Visualizing-3D-structures">¶</a></h3><p>Visualizing all the structures generated so far:</p>
+<p><a id="ions"></a></p>
+<hr/>
+<h2 id="Adding-ions">Adding ions<a class="anchor-link" href="#Adding-ions">¶</a></h2><p>Add ions to neutralize the <strong>protein structure</strong> charge</p>
+<ul>
+<li><a href="#ionsStep1">Step 1</a>: Creating portable binary run file for ion generation</li>
+<li><a href="#ionsStep2">Step 2</a>: Adding ions to <strong>neutralize</strong> the system</li>
+</ul>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
 <ul>
-<li>Original <strong>ligand PDB structure</strong> (left)</li>
-<li><strong>Ligand PDB structure</strong> with <strong>hydrogen atoms</strong> (middle)</li>
-<li><strong>Ligand PDB structure</strong> with <strong>hydrogen atoms energetically minimized</strong> (right)</li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp">Grompp</a> from <strong>biobb_gromacs.gromacs.grompp</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genion">Genion</a> from <strong>biobb_gromacs.gromacs.genion</strong></li>
 </ul>
+<hr/>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="ionsStep1"></a></p>
+<h3 id="Step-1:-Creating-portable-binary-run-file-for-ion-generation">Step 1: Creating portable binary run file for ion generation<a class="anchor-link" href="#Step-1:-Creating-portable-binary-run-file-for-ion-generation">¶</a></h3><p>A simple <strong>energy minimization</strong> molecular dynamics parameters (mdp) properties will be used to generate the portable binary run file for <strong>ion generation</strong>, although <strong>any legitimate combination of parameters</strong> could be used in this step.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Grompp: Creating portable binary run file for ion generation</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.grompp</span> <span class="kn">import</span> <span class="n">grompp</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_gppion_tpr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_gppion.tpr'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'minimization'</span><span class="p">,</span>
+    <span class="s1">'maxwarn'</span><span class="p">:</span> <span class="mi">1</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">grompp</span><span class="p">(</span><span class="n">input_gro_path</span><span class="o">=</span><span class="n">output_solvate_gro</span><span class="p">,</span> 
+       <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_solvate_top_zip</span><span class="p">,</span> 
+       <span class="n">output_tpr_path</span><span class="o">=</span><span class="n">output_gppion_tpr</span><span class="p">,</span>  
+       <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="ionsStep2"></a></p>
+<h3 id="Step-2:-Adding-ions-to-neutralize-the-system">Step 2: Adding ions to neutralize the system<a class="anchor-link" href="#Step-2:-Adding-ions-to-neutralize-the-system">¶</a></h3><p>Replace <strong>solvent molecules</strong> with <strong>ions</strong> to <strong>neutralize</strong> the system.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Genion: Adding ions to neutralize the system</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.genion</span> <span class="kn">import</span> <span class="n">genion</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_genion_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_genion.gro'</span>
+<span class="n">output_genion_top_zip</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_genion_top.zip'</span>
+<span class="n">prop</span><span class="o">=</span><span class="p">{</span>
+    <span class="s1">'neutral'</span><span class="p">:</span><span class="kc">True</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">genion</span><span class="p">(</span><span class="n">input_tpr_path</span><span class="o">=</span><span class="n">output_gppion_tpr</span><span class="p">,</span> 
+       <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_genion_gro</span><span class="p">,</span> 
+       <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_solvate_top_zip</span><span class="p">,</span> 
+       <span class="n">output_top_zip_path</span><span class="o">=</span><span class="n">output_genion_top_zip</span><span class="p">,</span> 
+       <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the <strong>neutralized protein system</strong> with the newly added <strong>ions</strong> using <strong>NGL</strong></p>
 </div>
 </div>
 </div>
@@ -7948,26 +8191,18 @@ <h3 id="Visualizing-3D-structures">Visualizing 3D structures<a class="anchor-lin
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1">#Show different structures generated (for comparison)</span>
-<span class="n">view1</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">input_structure</span><span class="p">)</span>
-<span class="n">view1</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">)</span>
-<span class="n">view1</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">'250px'</span><span class="p">,</span><span class="s1">'300px'</span><span class="p">])</span>
-<span class="n">view1</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
-<span class="n">view1</span>
-<span class="n">view2</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_babel_h</span><span class="p">)</span>
-<span class="n">view2</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">)</span>
-<span class="n">view2</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">'250px'</span><span class="p">,</span><span class="s1">'300px'</span><span class="p">])</span>
-<span class="n">view2</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
-<span class="n">view2</span>
-<span class="n">view3</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_babel_min</span><span class="p">)</span>
-<span class="n">view3</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">)</span>
-<span class="n">view3</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">'250px'</span><span class="p">,</span><span class="s1">'300px'</span><span class="p">])</span>
-<span class="n">view3</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
-<span class="n">view3</span>
-<span class="n">ipywidgets</span><span class="o">.</span><span class="n">HBox</span><span class="p">([</span><span class="n">view1</span><span class="p">,</span> <span class="n">view2</span><span class="p">,</span> <span class="n">view3</span><span class="p">])</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Show protein</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_genion_gro</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">clear_representations</span><span class="p">()</span>
+<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'cartoon'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'solute'</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">'sstruc'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'NA'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'CL'</span><span class="p">)</span>
+<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'600px'</span><span class="p">])</span>
+<span class="n">view</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
+<span class="n">view</span>
 </pre></div>
 </div>
 </div>
@@ -7980,9 +8215,7 @@ <h3 id="Visualizing-3D-structures">Visualizing 3D structures<a class="anchor-lin
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><img src='ngl4.png' style='float:left;width:33%;' id="64872ef8744165.93963572" data-dependant="true" data-width="300" data-height="400"></img>
-  <img src='ngl5.png' style='float:left;width:33%;' id="64872f317645b3.45578065" data-dependant="true" data-width="300" data-height="400"></img>
-  <img src='ngl6.png' style='float:left;width:33%;' id="64872f51f10ae8.42998441" data-slaves="64872ef8744165.93963572|64872f317645b3.45578065" data-width="300" data-height="400"></img></p>
+<p><img src='ngl5.png' id="64883cc5a687a1.83659086" data-width="600" data-height="450"></img></p>
 </div>
 </div>
 </div>
@@ -7993,47 +8226,70 @@ <h3 id="Visualizing-3D-structures">Visualizing 3D structures<a class="anchor-lin
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><a id="acpype"></a></p>
+<p><a id="min"></a></p>
 <hr/>
-<h2 id="Generating-ligand-parameters">Generating ligand parameters<a class="anchor-link" href="#Generating-ligand-parameters">¶</a></h2><p><strong>Building GROMACS topology</strong> corresponding to the <strong>ligand structure</strong>.</p>
-<p><strong>Force field</strong> used in this tutorial step is <strong>amberGAFF</strong>: <a href="http://ambermd.org/antechamber/gaff.html">General AMBER Force Field</a>, designed for rational drug design.</p>
+<h2 id="Energetically-minimize-the-system">Energetically minimize the system<a class="anchor-link" href="#Energetically-minimize-the-system">¶</a></h2><p>Energetically minimize the <strong>protein system</strong> till reaching a desired potential energy.</p>
+<ul>
+<li><a href="#emStep1">Step 1</a>: Creating portable binary run file for energy minimization</li>
+<li><a href="#emStep2">Step 2</a>: Energetically minimize the <strong>system</strong> till reaching a force of 500 kJ/mol*nm.</li>
+<li><a href="#emStep3">Step 3</a>: Checking <strong>energy minimization</strong> results. Plotting energy by time during the <strong>minimization</strong> process.</li>
+</ul>
 <hr/>
 <p><strong>Building Blocks</strong> used:</p>
 <ul>
-<li><a href="https://biobb-chemistry.readthedocs.io/en/latest/acpype.html#module-acpype.acpype_params_gmx">AcpypeParamsGMX</a> from <strong>biobb_chemistry.acpype.acpype_params_gmx</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp">Grompp</a> from <strong>biobb_gromacs.gromacs.grompp</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun">Mdrun</a> from <strong>biobb_gromacs.gromacs.mdrun</strong></li>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy">GMXEnergy</a> from <strong>biobb_analysis.gromacs.gmx_energy</strong></li>
 </ul>
 <hr/>
 </div>
 </div>
 </div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="emStep1"></a></p>
+<h3 id="Step-1:-Creating-portable-binary-run-file-for-energy-minimization">Step 1: Creating portable binary run file for energy minimization<a class="anchor-link" href="#Step-1:-Creating-portable-binary-run-file-for-energy-minimization">¶</a></h3><p>The <strong>minimization</strong> type of the <strong>molecular dynamics parameters (mdp) property</strong> contains the main default parameters to run an <strong>energy minimization</strong>:</p>
+<ul>
+<li>integrator  = steep ; Algorithm (steep = steepest descent minimization)</li>
+<li>emtol       = 1000.0 ; Stop minimization when the maximum force &lt; 1000.0 kJ/mol/nm</li>
+<li>emstep      = 0.01 ; Minimization step size (nm)</li>
+<li>nsteps      = 50000 ; Maximum number of (minimization) steps to perform</li>
+</ul>
+<p>In this particular example, the method used to run the <strong>energy minimization</strong> is the default <strong>steepest descent</strong>, but the <strong>maximum force</strong> is placed at <strong>500 kJ/mol*nm^2</strong>, and the <strong>maximum number of steps</strong> to perform (if the maximum force is not reached) to <strong>5,000 steps</strong>.</p>
+</div>
+</div>
+</div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
 <div class="jp-Cell-inputWrapper" tabindex="0">
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Acpype_params_gmx: Generation of topologies for GROMACS with ACPype</span>
-<span class="c1"># Import module</span>
-<span class="kn">from</span> <span class="nn">biobb_chemistry.acpype.acpype_params_gmx</span> <span class="kn">import</span> <span class="n">acpype_params_gmx</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Grompp: Creating portable binary run file for mdrun</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.grompp</span> <span class="kn">import</span> <span class="n">grompp</span>
 
 <span class="c1"># Create prop dict and inputs/outputs</span>
-<span class="n">output_acpype_gro</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'params.gro'</span>
-<span class="n">output_acpype_itp</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'params.itp'</span>
-<span class="n">output_acpype_top</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'params.top'</span>
-<span class="n">output_acpype</span> <span class="o">=</span> <span class="n">ligandCode</span> <span class="o">+</span> <span class="s1">'params'</span>
+<span class="n">output_gppmin_tpr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_gppmin.tpr'</span>
 <span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
-    <span class="s1">'basename'</span> <span class="p">:</span> <span class="n">output_acpype</span><span class="p">,</span>
-    <span class="s1">'charge'</span> <span class="p">:</span> <span class="n">mol_charge</span>
+    <span class="s1">'mdp'</span><span class="p">:{</span>
+        <span class="s1">'emtol'</span><span class="p">:</span><span class="s1">'500'</span><span class="p">,</span>
+        <span class="s1">'nsteps'</span><span class="p">:</span><span class="s1">'5000'</span>
+    <span class="p">},</span>
+    <span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'minimization'</span>
 <span class="p">}</span>
 
-<span class="c1">#Create and launch bb</span>
-<span class="n">acpype_params_gmx</span><span class="p">(</span><span class="n">input_path</span><span class="o">=</span><span class="n">output_babel_min</span><span class="p">,</span>
-                <span class="n">output_path_gro</span><span class="o">=</span><span class="n">output_acpype_gro</span><span class="p">,</span>
-                <span class="n">output_path_itp</span><span class="o">=</span><span class="n">output_acpype_itp</span><span class="p">,</span>
-                <span class="n">output_path_top</span><span class="o">=</span><span class="n">output_acpype_top</span><span class="p">,</span>
-                <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+<span class="c1"># Create and launch bb</span>
+<span class="n">grompp</span><span class="p">(</span><span class="n">input_gro_path</span><span class="o">=</span><span class="n">output_genion_gro</span><span class="p">,</span> 
+       <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_genion_top_zip</span><span class="p">,</span> 
+       <span class="n">output_tpr_path</span><span class="o">=</span><span class="n">output_gppmin_tpr</span><span class="p">,</span>  
+       <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -8046,7 +8302,8 @@ <h2 id="Generating-ligand-parameters">Generating ligand parameters<a class="anch
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link" href="#Visualizing-3D-structure">¶</a></h3><p>Visualizing the generated <strong>GROMACS</strong> gro structure corresponding to the parameterized <strong>ligand PDB structure</strong> using <strong>NGL</strong>:</p>
+<p><a id="emStep2"></a></p>
+<h3 id="Step-2:-Running-Energy-Minimization">Step 2: Running Energy Minimization<a class="anchor-link" href="#Step-2:-Running-Energy-Minimization">¶</a></h3><p>Running <strong>energy minimization</strong> using the <strong>tpr file</strong> generated in the previous step.</p>
 </div>
 </div>
 </div>
@@ -8055,15 +8312,98 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
 </div>
 <div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="c1">#Show small ligand structure</span>
-<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_structure_file</span><span class="p">(</span><span class="n">output_acpype_gro</span><span class="p">)</span>
-<span class="n">view</span><span class="o">.</span><span class="n">add_representation</span><span class="p">(</span><span class="n">repr_type</span><span class="o">=</span><span class="s1">'ball+stick'</span><span class="p">,</span> <span class="n">selection</span><span class="o">=</span><span class="s1">'all'</span><span class="p">)</span>
-<span class="n">view</span><span class="o">.</span><span class="n">_remote_call</span><span class="p">(</span><span class="s1">'setSize'</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="s1">'Widget'</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">''</span><span class="p">,</span><span class="s1">'300px'</span><span class="p">])</span>
-<span class="n">view</span><span class="o">.</span><span class="n">camera</span><span class="o">=</span><span class="s1">'orthographic'</span>
-<span class="n">view</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Mdrun: Running minimization</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.mdrun</span> <span class="kn">import</span> <span class="n">mdrun</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_min_trr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_min.trr'</span>
+<span class="n">output_min_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_min.gro'</span>
+<span class="n">output_min_edr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_min.edr'</span>
+<span class="n">output_min_log</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_min.log'</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">mdrun</span><span class="p">(</span><span class="n">input_tpr_path</span><span class="o">=</span><span class="n">output_gppmin_tpr</span><span class="p">,</span> 
+      <span class="n">output_trr_path</span><span class="o">=</span><span class="n">output_min_trr</span><span class="p">,</span> 
+      <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_min_gro</span><span class="p">,</span> 
+      <span class="n">output_edr_path</span><span class="o">=</span><span class="n">output_min_edr</span><span class="p">,</span> 
+      <span class="n">output_log_path</span><span class="o">=</span><span class="n">output_min_log</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="emStep3"></a></p>
+<h3 id="Step-3:-Checking-Energy-Minimization-results">Step 3: Checking Energy Minimization results<a class="anchor-link" href="#Step-3:-Checking-Energy-Minimization-results">¶</a></h3><p>Checking <strong>energy minimization</strong> results. Plotting <strong>potential energy</strong> by time during the minimization process.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXEnergy: Getting system energy by time  </span>
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_energy</span> <span class="kn">import</span> <span class="n">gmx_energy</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_min_ene_xvg</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_min_ene.xvg'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'terms'</span><span class="p">:</span>  <span class="p">[</span><span class="s2">"Potential"</span><span class="p">]</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_energy</span><span class="p">(</span><span class="n">input_energy_path</span><span class="o">=</span><span class="n">output_min_edr</span><span class="p">,</span> 
+          <span class="n">output_xvg_path</span><span class="o">=</span><span class="n">output_min_ene_xvg</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
+
+<span class="c1"># Read data from file and filter energy values higher than 1000 kJ/mol</span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_min_ene_xvg</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">energy_file</span><span class="p">:</span>
+    <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span>
+        <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">energy_file</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">"#"</span><span class="p">,</span> <span class="s2">"@"</span><span class="p">))</span>
+        <span class="k">if</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&lt;</span> <span class="mi">1000</span>
+    <span class="p">])</span>
+
+<span class="c1"># Create a scatter plot</span>
+<span class="n">fig</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Figure</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">'lines'</span><span class="p">))</span>
+
+<span class="c1"># Update layout</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">"Energy Minimization"</span><span class="p">,</span>
+                  <span class="n">xaxis_title</span><span class="o">=</span><span class="s2">"Energy Minimization Step"</span><span class="p">,</span>
+                  <span class="n">yaxis_title</span><span class="o">=</span><span class="s2">"Potential Energy kJ/mol"</span><span class="p">,</span>
+                  <span class="n">height</span><span class="o">=</span><span class="mi">600</span><span class="p">)</span>
+
+<span class="c1"># Show the figure (renderer changes for colab and jupyter)</span>
+<span class="n">rend</span> <span class="o">=</span> <span class="s1">'colab'</span> <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span> <span class="k">else</span> <span class="s1">''</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">renderer</span><span class="o">=</span><span class="n">rend</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -8076,7 +8416,7 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><img src='ngl7.png' id="648724a90561a8.76814527" data-width="500" data-height="250"></img></p>
+<p><img alt="No description has been provided for this image" src="plot1.png"/></p>
 </div>
 </div>
 </div>
@@ -8087,13 +8427,926 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><a id="output"></a></p>
-<h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
+<p><a id="nvt"></a></p>
+<hr/>
+<h2 id="Equilibrate-the-system-(NVT)">Equilibrate the system (NVT)<a class="anchor-link" href="#Equilibrate-the-system-(NVT)">¶</a></h2><p>Equilibrate the <strong>protein system</strong> in <strong>NVT ensemble</strong> (constant Number of particles, Volume and Temperature). Protein <strong>heavy atoms</strong> will be restrained using position restraining forces: movement is permitted, but only after overcoming a substantial energy penalty. The utility of position restraints is that they allow us to equilibrate our solvent around our protein, without the added variable of structural changes in the protein.</p>
+<ul>
+<li><a href="#eqNVTStep1">Step 1</a>: Creating portable binary run file for system equilibration</li>
+<li><a href="#eqNVTStep2">Step 2</a>: Equilibrate the <strong>protein system</strong> with <strong>NVT</strong> ensemble.</li>
+<li><a href="#eqNVTStep3">Step 3</a>: Checking <strong>NVT Equilibration</strong> results. Plotting <strong>system temperature</strong> by time during the <strong>NVT equilibration</strong> process.</li>
+</ul>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
 <ul>
-  <li>IBPparams.gro: <strong>Structure</strong> of the parameterized ligand in gro (GROMACS) format.</li>
-  <li>IBPparams.top: <strong>Topology</strong> of the parameterized ligand, including a reference to the IBPparams.itp.</li>
-  <li>IBPparams.itp: <strong>Include Topology File (itp)</strong> of the parameterized ligand, including the parameters information: bonds, angles, dihedrals, etc.</li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp">Grompp</a> from <strong>biobb_gromacs.gromacs.grompp</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun">Mdrun</a> from <strong>biobb_gromacs.gromacs.mdrun</strong></li>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy">GMXEnergy</a> from <strong>biobb_analysis.gromacs.gmx_energy</strong></li>
 </ul>
+<hr/>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="eqNVTStep1"></a></p>
+<h3 id="Step-1:-Creating-portable-binary-run-file-for-system-equilibration-(NVT)">Step 1: Creating portable binary run file for system equilibration (NVT)<a class="anchor-link" href="#Step-1:-Creating-portable-binary-run-file-for-system-equilibration-(NVT)">¶</a></h3><p>The <strong>nvt</strong> type of the <strong>molecular dynamics parameters (mdp) property</strong> contains the main default parameters to run an <strong>NVT equilibration</strong> with <strong>protein restraints</strong> (see <a href="http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html">GROMACS mdp options</a>):</p>
+<ul>
+<li>Define                   = -DPOSRES</li>
+<li>integrator               = md</li>
+<li>dt                       = 0.002</li>
+<li>nsteps                   = 5000</li>
+<li>pcoupl                   = no</li>
+<li>gen_vel                  = yes</li>
+<li>gen_temp                 = 300</li>
+<li>gen_seed                 = -1</li>
+</ul>
+<p>In this particular example, the default parameters will be used: <strong>md</strong> integrator algorithm, a <strong>step size</strong> of <strong>2fs</strong>, <strong>5,000 equilibration steps</strong> with the protein <strong>heavy atoms restrained</strong>, and a temperature of <strong>300K</strong>.</p>
+<p><em>Please note that for the sake of time this tutorial is only running 10ps of NVT equilibration, whereas in the <a href="http://www.mdtutorials.com/gmx/lysozyme/06_equil.html">original example</a> the simulated time was 100ps.</em></p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Grompp: Creating portable binary run file for NVT Equilibration</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.grompp</span> <span class="kn">import</span> <span class="n">grompp</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_gppnvt_tpr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_gppnvt.tpr'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'mdp'</span><span class="p">:{</span>
+        <span class="s1">'nsteps'</span><span class="p">:</span> <span class="mi">5000</span><span class="p">,</span>
+        <span class="s1">'dt'</span><span class="p">:</span> <span class="mf">0.002</span><span class="p">,</span>
+        <span class="s1">'Define'</span><span class="p">:</span> <span class="s1">'-DPOSRES'</span><span class="p">,</span>
+        <span class="c1">#'tc_grps': "DNA Water_and_ions" # NOTE: uncomment this line if working with DNA</span>
+    <span class="p">},</span>
+    <span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'nvt'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">grompp</span><span class="p">(</span><span class="n">input_gro_path</span><span class="o">=</span><span class="n">output_min_gro</span><span class="p">,</span> 
+       <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_genion_top_zip</span><span class="p">,</span> 
+       <span class="n">output_tpr_path</span><span class="o">=</span><span class="n">output_gppnvt_tpr</span><span class="p">,</span>  
+       <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="eqNVTStep2"></a></p>
+<h3 id="Step-2:-Running-NVT-equilibration">Step 2: Running NVT equilibration<a class="anchor-link" href="#Step-2:-Running-NVT-equilibration">¶</a></h3>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Mdrun: Running Equilibration NVT</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.mdrun</span> <span class="kn">import</span> <span class="n">mdrun</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_nvt_trr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_nvt.trr'</span>
+<span class="n">output_nvt_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_nvt.gro'</span>
+<span class="n">output_nvt_edr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_nvt.edr'</span>
+<span class="n">output_nvt_log</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_nvt.log'</span>
+<span class="n">output_nvt_cpt</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_nvt.cpt'</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">mdrun</span><span class="p">(</span><span class="n">input_tpr_path</span><span class="o">=</span><span class="n">output_gppnvt_tpr</span><span class="p">,</span> 
+      <span class="n">output_trr_path</span><span class="o">=</span><span class="n">output_nvt_trr</span><span class="p">,</span> 
+      <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_nvt_gro</span><span class="p">,</span> 
+      <span class="n">output_edr_path</span><span class="o">=</span><span class="n">output_nvt_edr</span><span class="p">,</span> 
+      <span class="n">output_log_path</span><span class="o">=</span><span class="n">output_nvt_log</span><span class="p">,</span> 
+      <span class="n">output_cpt_path</span><span class="o">=</span><span class="n">output_nvt_cpt</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="eqNVTStep3"></a></p>
+<h3 id="Step-3:-Checking-NVT-Equilibration-results">Step 3: Checking NVT Equilibration results<a class="anchor-link" href="#Step-3:-Checking-NVT-Equilibration-results">¶</a></h3><p>Checking <strong>NVT Equilibration</strong> results. Plotting <strong>system temperature</strong> by time during the NVT equilibration process.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXEnergy: Getting system temperature by time during NVT Equilibration  </span>
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_energy</span> <span class="kn">import</span> <span class="n">gmx_energy</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_nvt_temp_xvg</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_nvt_temp.xvg'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'terms'</span><span class="p">:</span>  <span class="p">[</span><span class="s2">"Temperature"</span><span class="p">]</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_energy</span><span class="p">(</span><span class="n">input_energy_path</span><span class="o">=</span><span class="n">output_nvt_edr</span><span class="p">,</span> 
+          <span class="n">output_xvg_path</span><span class="o">=</span><span class="n">output_nvt_temp_xvg</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
+
+<span class="c1"># Read temperature data from file</span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_nvt_temp_xvg</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">temperature_file</span><span class="p">:</span>
+    <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span>
+        <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">temperature_file</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">"#"</span><span class="p">,</span> <span class="s2">"@"</span><span class="p">))</span>
+    <span class="p">])</span>
+
+<span class="c1"># Create a scatter plot</span>
+<span class="n">fig</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Figure</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">'lines+markers'</span><span class="p">))</span>
+
+<span class="c1"># Update layout</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">"Temperature during NVT Equilibration"</span><span class="p">,</span>
+                  <span class="n">xaxis_title</span><span class="o">=</span><span class="s2">"Time (ps)"</span><span class="p">,</span>
+                  <span class="n">yaxis_title</span><span class="o">=</span><span class="s2">"Temperature (K)"</span><span class="p">,</span>
+                  <span class="n">height</span><span class="o">=</span><span class="mi">600</span><span class="p">)</span>
+
+<span class="c1"># Show the figure (renderer changes for colab and jupyter)</span>
+<span class="n">rend</span> <span class="o">=</span> <span class="s1">'colab'</span> <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span> <span class="k">else</span> <span class="s1">''</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">renderer</span><span class="o">=</span><span class="n">rend</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><img alt="No description has been provided for this image" src="plot2.png"/></p>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="npt"></a></p>
+<hr/>
+<h2 id="Equilibrate-the-system-(NPT)">Equilibrate the system (NPT)<a class="anchor-link" href="#Equilibrate-the-system-(NPT)">¶</a></h2><p>Equilibrate the <strong>protein system</strong> in <strong>NPT</strong> ensemble (constant Number of particles, Pressure and Temperature).</p>
+<ul>
+<li><a href="#eqNPTStep1">Step 1</a>: Creating portable binary run file for system equilibration</li>
+<li><a href="#eqNPTStep2">Step 2</a>: Equilibrate the <strong>protein system</strong> with <strong>NPT</strong> ensemble.</li>
+<li><a href="#eqNPTStep3">Step 3</a>: Checking <strong>NPT Equilibration</strong> results. Plotting <strong>system pressure and density</strong> by time during the <strong>NPT equilibration</strong> process.</li>
+</ul>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
+<ul>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp">Grompp</a> from <strong>biobb_gromacs.gromacs.grompp</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun">Mdrun</a> from <strong>biobb_gromacs.gromacs.mdrun</strong></li>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy">GMXEnergy</a> from <strong>biobb_analysis.gromacs.gmx_energy</strong></li>
+</ul>
+<hr/>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="eqNPTStep1"></a></p>
+<h3 id="Step-1:-Creating-portable-binary-run-file-for-system-equilibration-(NPT)">Step 1: Creating portable binary run file for system equilibration (NPT)<a class="anchor-link" href="#Step-1:-Creating-portable-binary-run-file-for-system-equilibration-(NPT)">¶</a></h3><p>The <strong>npt</strong> type of the <strong>molecular dynamics parameters (mdp) property</strong> contains the main default parameters to run an <strong>NPT equilibration</strong> with <strong>protein restraints</strong> (see <a href="http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html">GROMACS mdp options</a>):</p>
+<ul>
+<li>Define                   = -DPOSRES</li>
+<li>integrator               = md</li>
+<li>dt                       = 0.002</li>
+<li>nsteps                   = 5000</li>
+<li>pcoupl = Parrinello-Rahman</li>
+<li>pcoupltype = isotropic</li>
+<li>tau_p = 1.0</li>
+<li>ref_p = 1.0</li>
+<li>compressibility = 4.5e-5</li>
+<li>refcoord_scaling = com</li>
+<li>gen_vel = no</li>
+</ul>
+<p>In this particular example, the default parameters will be used: <strong>md</strong> integrator algorithm, a <strong>time step</strong> of <strong>2fs</strong>, <strong>5,000 equilibration steps</strong> with the protein <strong>heavy atoms restrained</strong>, and a Parrinello-Rahman <strong>pressure coupling</strong> algorithm.</p>
+<p><em>Please note that for the sake of time this tutorial is only running 10ps of NPT equilibration, whereas in the <a href="http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html">original example</a> the simulated time was 100ps.</em></p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Grompp: Creating portable binary run file for NPT System Equilibration</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.grompp</span> <span class="kn">import</span> <span class="n">grompp</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_gppnpt_tpr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_gppnpt.tpr'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'mdp'</span><span class="p">:{</span>
+        <span class="s1">'nsteps'</span><span class="p">:</span><span class="s1">'5000'</span><span class="p">,</span>
+        <span class="c1">#'tc_grps': "DNA Water_and_ions" # NOTE: uncomment this line if working with DNA</span>
+    <span class="p">},</span>
+    <span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'npt'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">grompp</span><span class="p">(</span><span class="n">input_gro_path</span><span class="o">=</span><span class="n">output_nvt_gro</span><span class="p">,</span> 
+       <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_genion_top_zip</span><span class="p">,</span> 
+       <span class="n">output_tpr_path</span><span class="o">=</span><span class="n">output_gppnpt_tpr</span><span class="p">,</span> 
+       <span class="n">input_cpt_path</span><span class="o">=</span><span class="n">output_nvt_cpt</span><span class="p">,</span>  
+       <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="eqNPTStep2"></a></p>
+<h3 id="Step-2:-Running-NPT-equilibration">Step 2: Running NPT equilibration<a class="anchor-link" href="#Step-2:-Running-NPT-equilibration">¶</a></h3>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Mdrun: Running NPT System Equilibration</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.mdrun</span> <span class="kn">import</span> <span class="n">mdrun</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_npt_trr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_npt.trr'</span>
+<span class="n">output_npt_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_npt.gro'</span>
+<span class="n">output_npt_edr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_npt.edr'</span>
+<span class="n">output_npt_log</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_npt.log'</span>
+<span class="n">output_npt_cpt</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_npt.cpt'</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">mdrun</span><span class="p">(</span><span class="n">input_tpr_path</span><span class="o">=</span><span class="n">output_gppnpt_tpr</span><span class="p">,</span> 
+      <span class="n">output_trr_path</span><span class="o">=</span><span class="n">output_npt_trr</span><span class="p">,</span> 
+      <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_npt_gro</span><span class="p">,</span> 
+      <span class="n">output_edr_path</span><span class="o">=</span><span class="n">output_npt_edr</span><span class="p">,</span> 
+      <span class="n">output_log_path</span><span class="o">=</span><span class="n">output_npt_log</span><span class="p">,</span> 
+      <span class="n">output_cpt_path</span><span class="o">=</span><span class="n">output_npt_cpt</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="eqNPTStep3"></a></p>
+<h3 id="Step-3:-Checking-NPT-Equilibration-results">Step 3: Checking NPT Equilibration results<a class="anchor-link" href="#Step-3:-Checking-NPT-Equilibration-results">¶</a></h3><p>Checking <strong>NPT Equilibration</strong> results. Plotting <strong>system pressure and density</strong> by time during the <strong>NPT equilibration</strong> process.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXEnergy: Getting system pressure and density by time during NPT Equilibration  </span>
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_energy</span> <span class="kn">import</span> <span class="n">gmx_energy</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_npt_pd_xvg</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_npt_PD.xvg'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'terms'</span><span class="p">:</span>  <span class="p">[</span><span class="s2">"Pressure"</span><span class="p">,</span><span class="s2">"Density"</span><span class="p">]</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_energy</span><span class="p">(</span><span class="n">input_energy_path</span><span class="o">=</span><span class="n">output_npt_edr</span><span class="p">,</span> 
+          <span class="n">output_xvg_path</span><span class="o">=</span><span class="n">output_npt_pd_xvg</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
+<span class="kn">from</span> <span class="nn">plotly.subplots</span> <span class="kn">import</span> <span class="n">make_subplots</span>
+
+<span class="c1"># Read pressure and density data from file </span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_npt_pd_xvg</span><span class="p">,</span><span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">pd_file</span><span class="p">:</span>
+    <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span>
+        <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">2</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">pd_file</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">"#"</span><span class="p">,</span> <span class="s2">"@"</span><span class="p">))</span>
+    <span class="p">])</span>
+
+<span class="n">trace1</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span>
+    <span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="o">=</span><span class="n">y</span>
+<span class="p">)</span>
+<span class="n">trace2</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span>
+    <span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="o">=</span><span class="n">z</span>
+<span class="p">)</span>
+
+<span class="n">fig</span> <span class="o">=</span> <span class="n">make_subplots</span><span class="p">(</span><span class="n">rows</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">cols</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">print_grid</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">append_trace</span><span class="p">(</span><span class="n">trace1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">append_trace</span><span class="p">(</span><span class="n">trace2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+
+<span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span>
+    <span class="n">height</span><span class="o">=</span><span class="mi">500</span><span class="p">,</span>
+    <span class="n">title</span><span class="o">=</span><span class="s1">'Pressure and Density during NPT Equilibration'</span><span class="p">,</span>
+    <span class="n">showlegend</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+    <span class="n">xaxis1_title</span><span class="o">=</span><span class="s1">'Time (ps)'</span><span class="p">,</span>
+    <span class="n">yaxis1_title</span><span class="o">=</span><span class="s1">'Pressure (bar)'</span><span class="p">,</span>
+    <span class="n">xaxis2_title</span><span class="o">=</span><span class="s1">'Time (ps)'</span><span class="p">,</span>
+    <span class="n">yaxis2_title</span><span class="o">=</span><span class="s1">'Density (Kg*m^-3)'</span>
+<span class="p">)</span>
+
+<span class="c1"># Show the figure (renderer changes for colab and jupyter)</span>
+<span class="n">rend</span> <span class="o">=</span> <span class="s1">'colab'</span> <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span> <span class="k">else</span> <span class="s1">''</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">renderer</span><span class="o">=</span><span class="n">rend</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><img alt="No description has been provided for this image" src="plot3.png"/></p>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="free"></a></p>
+<hr/>
+<h2 id="Free-Molecular-Dynamics-Simulation">Free Molecular Dynamics Simulation<a class="anchor-link" href="#Free-Molecular-Dynamics-Simulation">¶</a></h2><p>Upon completion of the <strong>two equilibration phases (NVT and NPT)</strong>, the system is now well-equilibrated at the desired temperature and pressure. The <strong>position restraints</strong> can now be released. The last step of the <strong>protein</strong> MD setup is a short, <strong>free MD simulation</strong>, to ensure the robustness of the system.</p>
+<ul>
+<li><a href="#mdStep1">Step 1</a>: Creating portable binary run file to run a <strong>free MD simulation</strong>.</li>
+<li><a href="#mdStep2">Step 2</a>: Run short MD simulation of the <strong>protein system</strong>.</li>
+<li><a href="#mdStep3">Step 3</a>: Checking results for the final step of the setup process, the <strong>free MD run</strong>. Plotting <strong>Root Mean Square deviation (RMSd)</strong> and <strong>Radius of Gyration (Rgyr)</strong> by time during the <strong>free MD run</strong> step.</li>
+</ul>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
+<ul>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp">Grompp</a> from <strong>biobb_gromacs.gromacs.grompp</strong></li>
+<li><a href="https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun">Mdrun</a> from <strong>biobb_gromacs.gromacs.mdrun</strong></li>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_rms">GMXRms</a> from <strong>biobb_analysis.gromacs.gmx_rms</strong></li>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_rgyr">GMXRgyr</a> from <strong>biobb_analysis.gromacs.gmx_rgyr</strong></li>
+</ul>
+<hr/>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="mdStep1"></a></p>
+<h3 id="Step-1:-Creating-portable-binary-run-file-to-run-a-free-MD-simulation">Step 1: Creating portable binary run file to run a free MD simulation<a class="anchor-link" href="#Step-1:-Creating-portable-binary-run-file-to-run-a-free-MD-simulation">¶</a></h3><p>The <strong>free</strong> type of the <strong>molecular dynamics parameters (mdp) property</strong> contains the main default parameters to run an <strong>free MD simulation</strong> (see <a href="http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html">GROMACS mdp options</a>):</p>
+<ul>
+<li>integrator               = md</li>
+<li>dt                       = 0.002 (ps)</li>
+<li>nsteps                   = 50000</li>
+</ul>
+<p>In this particular example, the default parameters will be used: <strong>md</strong> integrator algorithm, a <strong>time step</strong> of <strong>2fs</strong>, and a total of <strong>50,000 md steps</strong> (100ps).</p>
+<p><em>Please note that for the sake of time this tutorial is only running 100ps of free MD, whereas in the <a href="http://www.mdtutorials.com/gmx/lysozyme/08_MD.html">original example</a> the simulated time was 1ns (1000ps).</em></p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Grompp: Creating portable binary run file for mdrun</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.grompp</span> <span class="kn">import</span> <span class="n">grompp</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_gppmd_tpr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_gppmd.tpr'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'mdp'</span><span class="p">:{</span>
+        <span class="s1">'nsteps'</span><span class="p">:</span><span class="s1">'50000'</span><span class="p">,</span>
+        <span class="c1">#'tc_grps': "DNA Water_and_ions" # NOTE: uncomment this line if working with DNA</span>
+    <span class="p">},</span>
+    <span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'free'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">grompp</span><span class="p">(</span><span class="n">input_gro_path</span><span class="o">=</span><span class="n">output_npt_gro</span><span class="p">,</span> 
+       <span class="n">input_top_zip_path</span><span class="o">=</span><span class="n">output_genion_top_zip</span><span class="p">,</span> 
+       <span class="n">output_tpr_path</span><span class="o">=</span><span class="n">output_gppmd_tpr</span><span class="p">,</span> 
+       <span class="n">input_cpt_path</span><span class="o">=</span><span class="n">output_npt_cpt</span><span class="p">,</span> 
+       <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="mdStep2"></a></p>
+<h3 id="Step-2:-Running-short-free-MD-simulation">Step 2: Running short free MD simulation<a class="anchor-link" href="#Step-2:-Running-short-free-MD-simulation">¶</a></h3>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Mdrun: Running free dynamics</span>
+<span class="kn">from</span> <span class="nn">biobb_gromacs.gromacs.mdrun</span> <span class="kn">import</span> <span class="n">mdrun</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_md_trr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_md.trr'</span>
+<span class="n">output_md_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_md.gro'</span>
+<span class="n">output_md_edr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_md.edr'</span>
+<span class="n">output_md_log</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_md.log'</span>
+<span class="n">output_md_cpt</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_md.cpt'</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">mdrun</span><span class="p">(</span><span class="n">input_tpr_path</span><span class="o">=</span><span class="n">output_gppmd_tpr</span><span class="p">,</span> 
+      <span class="n">output_trr_path</span><span class="o">=</span><span class="n">output_md_trr</span><span class="p">,</span> 
+      <span class="n">output_gro_path</span><span class="o">=</span><span class="n">output_md_gro</span><span class="p">,</span> 
+      <span class="n">output_edr_path</span><span class="o">=</span><span class="n">output_md_edr</span><span class="p">,</span> 
+      <span class="n">output_log_path</span><span class="o">=</span><span class="n">output_md_log</span><span class="p">,</span> 
+      <span class="n">output_cpt_path</span><span class="o">=</span><span class="n">output_md_cpt</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="mdStep3"></a></p>
+<h3 id="Step-3:-Checking-free-MD-simulation-results">Step 3: Checking free MD simulation results<a class="anchor-link" href="#Step-3:-Checking-free-MD-simulation-results">¶</a></h3><p>Checking results for the final step of the setup process, the <strong>free MD run</strong>. Plotting <strong>Root Mean Square deviation (RMSd)</strong> and <strong>Radius of Gyration (Rgyr)</strong> by time during the <strong>free MD run</strong> step. <strong>RMSd</strong> against the <strong>experimental structure</strong> (input structure of the pipeline) and against the <strong>minimized and equilibrated structure</strong> (output structure of the NPT equilibration step).</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXRms: Computing Root Mean Square deviation to analyse structural stability </span>
+<span class="c1">#         RMSd against minimized and equilibrated snapshot (backbone atoms)   </span>
+
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_rms</span> <span class="kn">import</span> <span class="n">gmx_rms</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_rms_first</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_rms_first.xvg'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'selection'</span><span class="p">:</span>  <span class="s1">'Backbone'</span><span class="p">,</span>
+    <span class="c1">#'selection': 'non-Water'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_rms</span><span class="p">(</span><span class="n">input_structure_path</span><span class="o">=</span><span class="n">output_gppmd_tpr</span><span class="p">,</span>
+         <span class="n">input_traj_path</span><span class="o">=</span><span class="n">output_md_trr</span><span class="p">,</span>
+         <span class="n">output_xvg_path</span><span class="o">=</span><span class="n">output_rms_first</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXRms: Computing Root Mean Square deviation to analyse structural stability </span>
+<span class="c1">#         RMSd against experimental structure (backbone atoms)   </span>
+
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_rms</span> <span class="kn">import</span> <span class="n">gmx_rms</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_rms_exp</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_rms_exp.xvg'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'selection'</span><span class="p">:</span>  <span class="s1">'Backbone'</span><span class="p">,</span>
+    <span class="c1">#'selection': 'non-Water'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_rms</span><span class="p">(</span><span class="n">input_structure_path</span><span class="o">=</span><span class="n">output_gppmin_tpr</span><span class="p">,</span>
+         <span class="n">input_traj_path</span><span class="o">=</span><span class="n">output_md_trr</span><span class="p">,</span>
+         <span class="n">output_xvg_path</span><span class="o">=</span><span class="n">output_rms_exp</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
+
+<span class="c1"># Read RMS vs first snapshot data from file </span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_rms_first</span><span class="p">,</span><span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">rms_first_file</span><span class="p">:</span>
+    <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span>
+        <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rms_first_file</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">"#"</span><span class="p">,</span> <span class="s2">"@"</span><span class="p">))</span>
+    <span class="p">])</span>
+
+<span class="c1"># Read RMS vs experimental structure data from file </span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_rms_exp</span><span class="p">,</span><span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">rms_exp_file</span><span class="p">:</span>
+    <span class="n">x2</span><span class="p">,</span> <span class="n">y2</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span>
+        <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rms_exp_file</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">"#"</span><span class="p">,</span> <span class="s2">"@"</span><span class="p">))</span>
+    <span class="p">])</span>
+
+<span class="n">fig</span> <span class="o">=</span> <span class="n">make_subplots</span><span class="p">()</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">add_trace</span><span class="p">(</span><span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">"lines+markers"</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"RMSd vs first"</span><span class="p">))</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">add_trace</span><span class="p">(</span><span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y2</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">"lines+markers"</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"RMSd vs exp"</span><span class="p">))</span>
+
+<span class="c1"># Set layout including height</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span>
+    <span class="n">title</span><span class="o">=</span><span class="s2">"RMSd during free MD Simulation"</span><span class="p">,</span>
+    <span class="n">xaxis</span><span class="o">=</span><span class="nb">dict</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">"Time (ps)"</span><span class="p">),</span>
+    <span class="n">yaxis</span><span class="o">=</span><span class="nb">dict</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">"RMSd (nm)"</span><span class="p">),</span>
+    <span class="n">height</span><span class="o">=</span><span class="mi">600</span>
+<span class="p">)</span>
+
+<span class="c1"># Show the figure (renderer changes for colab and jupyter)</span>
+<span class="n">rend</span> <span class="o">=</span> <span class="s1">'colab'</span> <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span> <span class="k">else</span> <span class="s1">''</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">renderer</span><span class="o">=</span><span class="n">rend</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><img alt="No description has been provided for this image" src="plot4.png"/></p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXRgyr: Computing Radius of Gyration to measure the protein compactness during the free MD simulation </span>
+
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_rgyr</span> <span class="kn">import</span> <span class="n">gmx_rgyr</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_rgyr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_rgyr.xvg'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'selection'</span><span class="p">:</span>  <span class="s1">'Backbone'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_rgyr</span><span class="p">(</span><span class="n">input_structure_path</span><span class="o">=</span><span class="n">output_gppmin_tpr</span><span class="p">,</span>
+         <span class="n">input_traj_path</span><span class="o">=</span><span class="n">output_md_trr</span><span class="p">,</span>
+         <span class="n">output_xvg_path</span><span class="o">=</span><span class="n">output_rgyr</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
+
+<span class="c1"># Read Rgyr data from file</span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_rgyr</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">rgyr_file</span><span class="p">:</span>
+    <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span>
+        <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rgyr_file</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">"#"</span><span class="p">,</span> <span class="s2">"@"</span><span class="p">))</span>
+    <span class="p">])</span>
+
+<span class="c1"># Create a scatter plot</span>
+<span class="n">fig</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Figure</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">'lines+markers'</span><span class="p">))</span>
+
+<span class="c1"># Update layout</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">"Radius of Gyration"</span><span class="p">,</span>
+                  <span class="n">xaxis_title</span><span class="o">=</span><span class="s2">"Time (ps)"</span><span class="p">,</span>
+                  <span class="n">yaxis_title</span><span class="o">=</span><span class="s2">"Rgyr (nm)"</span><span class="p">,</span>
+                  <span class="n">height</span><span class="o">=</span><span class="mi">600</span><span class="p">)</span>
+
+<span class="c1"># Show the figure (renderer changes for colab and jupyter)</span>
+<span class="n">rend</span> <span class="o">=</span> <span class="s1">'colab'</span> <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span> <span class="k">else</span> <span class="s1">''</span>
+<span class="n">fig</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">renderer</span><span class="o">=</span><span class="n">rend</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><img alt="No description has been provided for this image" src="plot5.png"/></p>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="post"></a></p>
+<hr/>
+<h2 id="Post-processing-and-Visualizing-resulting-3D-trajectory">Post-processing and Visualizing resulting 3D trajectory<a class="anchor-link" href="#Post-processing-and-Visualizing-resulting-3D-trajectory">¶</a></h2><p>Post-processing and Visualizing the <strong>protein system</strong> MD setup <strong>resulting trajectory</strong> using <strong>NGL</strong></p>
+<ul>
+<li><a href="#ppStep1">Step 1</a>: <em>Imaging</em> the resulting trajectory, <strong>stripping out water molecules and ions</strong> and <strong>correcting periodicity issues</strong>.</li>
+<li><a href="#ppStep2">Step 2</a>: Generating a <em>dry</em> structure, <strong>removing water molecules and ions</strong> from the final snapshot of the MD setup pipeline.</li>
+<li><a href="#ppStep3">Step 3</a>: Visualizing the <em>imaged</em> trajectory using the <em>dry</em> structure as a <strong>topology</strong>.</li>
+</ul>
+<hr/>
+<p><strong>Building Blocks</strong> used:</p>
+<ul>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_image">GMXImage</a> from <strong>biobb_analysis.gromacs.gmx_image</strong></li>
+<li><a href="https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_trjconv_str">GMXTrjConvStr</a> from <strong>biobb_analysis.gromacs.gmx_trjconv_str</strong></li>
+</ul>
+<hr/>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="ppStep1"></a></p>
+<h3 id="Step-1:-Imaging-the-resulting-trajectory.">Step 1: <em>Imaging</em> the resulting trajectory.<a class="anchor-link" href="#Step-1:-Imaging-the-resulting-trajectory.">¶</a></h3><p>Stripping out <strong>water molecules and ions</strong> and <strong>correcting periodicity issues</strong></p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXImage: "Imaging" the resulting trajectory</span>
+<span class="c1">#           Removing water molecules and ions from the resulting structure</span>
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_image</span> <span class="kn">import</span> <span class="n">gmx_image</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_imaged_traj</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_imaged_traj.trr'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'center_selection'</span><span class="p">:</span>  <span class="s1">'Protein'</span><span class="p">,</span>
+    <span class="s1">'output_selection'</span><span class="p">:</span> <span class="s1">'Protein'</span><span class="p">,</span>
+    <span class="s1">'pbc'</span> <span class="p">:</span> <span class="s1">'mol'</span><span class="p">,</span>
+    <span class="s1">'center'</span> <span class="p">:</span> <span class="kc">True</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_image</span><span class="p">(</span><span class="n">input_traj_path</span><span class="o">=</span><span class="n">output_md_trr</span><span class="p">,</span>
+         <span class="n">input_top_path</span><span class="o">=</span><span class="n">output_gppmd_tpr</span><span class="p">,</span>
+         <span class="n">output_traj_path</span><span class="o">=</span><span class="n">output_imaged_traj</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="ppStep2"></a></p>
+<h3 id="Step-2:-Generating-the-output-dry-structure.">Step 2: Generating the output <em>dry</em> structure.<a class="anchor-link" href="#Step-2:-Generating-the-output-dry-structure.">¶</a></h3><p><strong>Removing water molecules and ions</strong> from the resulting structure</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># GMXTrjConvStr: Converting and/or manipulating a structure</span>
+<span class="c1">#                Removing water molecules and ions from the resulting structure</span>
+<span class="c1">#                The "dry" structure will be used as a topology to visualize </span>
+<span class="c1">#                the "imaged dry" trajectory generated in the previous step.</span>
+<span class="kn">from</span> <span class="nn">biobb_analysis.gromacs.gmx_trjconv_str</span> <span class="kn">import</span> <span class="n">gmx_trjconv_str</span>
+
+<span class="c1"># Create prop dict and inputs/outputs</span>
+<span class="n">output_dry_gro</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_md_dry.gro'</span>
+<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">'selection'</span><span class="p">:</span>  <span class="s1">'Protein'</span>
+<span class="p">}</span>
+
+<span class="c1"># Create and launch bb</span>
+<span class="n">gmx_trjconv_str</span><span class="p">(</span><span class="n">input_structure_path</span><span class="o">=</span><span class="n">output_md_gro</span><span class="p">,</span>
+         <span class="n">input_top_path</span><span class="o">=</span><span class="n">output_gppmd_tpr</span><span class="p">,</span>
+         <span class="n">output_str_path</span><span class="o">=</span><span class="n">output_dry_gro</span><span class="p">,</span> 
+          <span class="n">properties</span><span class="o">=</span><span class="n">prop</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="ppStep3"></a></p>
+<h3 id="Step-3:-Visualizing-the-generated-dehydrated-trajectory.">Step 3: Visualizing the generated dehydrated trajectory.<a class="anchor-link" href="#Step-3:-Visualizing-the-generated-dehydrated-trajectory.">¶</a></h3><p>Using the <strong>imaged trajectory</strong> (output of the <a href="#ppStep1">Post-processing step 1</a>) with the <strong>dry structure</strong> (output of the <a href="#ppStep2">Post-processing step 2</a>) as a topology.</p>
+</div>
+</div>
+</div>
+</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea">
+<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+<div class="cm-editor cm-s-jupyter">
+<div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Show trajectory</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_simpletraj</span><span class="p">(</span><span class="n">nglview</span><span class="o">.</span><span class="n">SimpletrajTrajectory</span><span class="p">(</span><span class="n">output_imaged_traj</span><span class="p">,</span> <span class="n">output_dry_gro</span><span class="p">),</span> <span class="n">gui</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<span class="n">view</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><img src='trajectory.gif' id="6489d524461bf6.23755072" data-width="700" data-height="550"></img></p>
+</div>
+</div>
+</div>
+</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<p><a id="output"></a></p>
+<h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
+<ul>
+  <li>1AKI_md.gro: <strong>Final structure</strong> (snapshot) of the MD setup protocol.</li>
+  <li>1AKI_md.trr: <strong>Final trajectory</strong> of the MD setup protocol.</li>
+  <li>1AKI_md.cpt: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
+  <li>1AKI_gppmd.tpr: <strong>Final tpr file</strong>, GROMACS portable binary run input file. This file contains the starting structure of the <strong>MD setup free MD simulation step</strong>, together with the molecular topology and all the simulation parameters. It can be used to <strong>extend</strong> the simulation.</li>
+  <li>1AKI_genion_top.zip: <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliary <strong>include topology</strong> files (.itp).</li>
+  </ul>
+  <p><strong>Analysis</strong> (MD setup check) output files generated:</p>
+  <ul>
+  <li>1AKI_rms_first.xvg: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
+  <li>1AKI_rms_exp.xvg: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
+  <li>1AKI_rgyr.xvg: <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
+  </ul>
 </div>
 </div>
 </div>
@@ -8125,4 +9378,4 @@ <h2 id="Questions-&amp;-Comments">Questions &amp; Comments<a class="anchor-link"
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