From 01e19b385ecb078d3785a519c8e4a3f4366475bf Mon Sep 17 00:00:00 2001
From: gbayarri <genis.bayarri@irbbarcelona.org>
Date: Mon, 3 Jun 2024 11:40:15 +0200
Subject: [PATCH] Unifying names

---
 .gitignore                                    |    2 +-
 README.md                                     |   10 +-
 biobb_wf_md_setup/docs/source/readme.md       |   10 +-
 biobb_wf_md_setup/docs/source/tutorial.md     |    2 +-
 .../html/biobb_wf_md_setup.web.html           |    4 +-
 .../html/biobb_wf_md_setup.web.ipynb          | 1541 -----------------
 .../notebooks/biobb_wf_md_setup.ipynb         |    2 +-
 7 files changed, 15 insertions(+), 1556 deletions(-)
 delete mode 100644 biobb_wf_md_setup/html/biobb_wf_md_setup.web.ipynb

diff --git a/.gitignore b/.gitignore
index b7adb03..6594e50 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,7 +19,7 @@ biobb_wf_md_setup/notebooks/*.gif
 biobb_wf_md_setup/notebooks/*.web.ipynb
 biobb_wf_md_setup/notebooks/*.docs.ipynb
 biobb_wf_md_setup/docs/notebooks
-biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.ipynb
+biobb_wf_md_setup/html/biobb_wf_md_setup.web.ipynb
 *.old.ipynb
 *.bk.ipynb
 \#*\#
diff --git a/README.md b/README.md
index 5fd4685..01e0864 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 [![](https://readthedocs.org/projects/biobb-wf-md-setup/badge/?version=latest)](https://biobb-wf-md-setup.readthedocs.io/en/latest/?badge=latest)
-[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb)
-[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb)
+[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAFkAAABZCAMAAABi1XidAAAB8lBMVEX///9XmsrmZYH1olJXmsr1olJXmsrmZYH1olJXmsr1olJXmsrmZYH1olL1olJXmsr1olJXmsrmZYH1olL1olJXmsrmZYH1olJXmsr1olL1olJXmsrmZYH1olL1olJXmsrmZYH1olL1olL0nFf1olJXmsrmZYH1olJXmsq8dZb1olJXmsrmZYH1olJXmspXmspXmsr1olL1olJXmsrmZYH1olJXmsr1olL1olJXmsrmZYH1olL1olLeaIVXmsrmZYH1olL1olL1olJXmsrmZYH1olLna31Xmsr1olJXmsr1olJXmsrmZYH1olLqoVr1olJXmsr1olJXmsrmZYH1olL1olKkfaPobXvviGabgadXmsqThKuofKHmZ4Dobnr1olJXmsr1olJXmspXmsr1olJXmsrfZ4TuhWn1olL1olJXmsqBi7X1olJXmspZmslbmMhbmsdemsVfl8ZgmsNim8Jpk8F0m7R4m7F5nLB6jbh7jbiDirOEibOGnKaMhq+PnaCVg6qWg6qegKaff6WhnpKofKGtnomxeZy3noG6dZi+n3vCcpPDcpPGn3bLb4/Mb47UbIrVa4rYoGjdaIbeaIXhoWHmZYHobXvpcHjqdHXreHLroVrsfG/uhGnuh2bwj2Hxk17yl1vzmljzm1j0nlX1olL3AJXWAAAAbXRSTlMAEBAQHx8gICAuLjAwMDw9PUBAQEpQUFBXV1hgYGBkcHBwcXl8gICAgoiIkJCQlJicnJ2goKCmqK+wsLC4usDAwMjP0NDQ1NbW3Nzg4ODi5+3v8PDw8/T09PX29vb39/f5+fr7+/z8/Pz9/v7+zczCxgAABC5JREFUeAHN1ul3k0UUBvCb1CTVpmpaitAGSLSpSuKCLWpbTKNJFGlcSMAFF63iUmRccNG6gLbuxkXU66JAUef/9LSpmXnyLr3T5AO/rzl5zj137p136BISy44fKJXuGN/d19PUfYeO67Znqtf2KH33Id1psXoFdW30sPZ1sMvs2D060AHqws4FHeJojLZqnw53cmfvg+XR8mC0OEjuxrXEkX5ydeVJLVIlV0e10PXk5k7dYeHu7Cj1j+49uKg7uLU61tGLw1lq27ugQYlclHC4bgv7VQ+TAyj5Zc/UjsPvs1sd5cWryWObtvWT2EPa4rtnWW3JkpjggEpbOsPr7F7EyNewtpBIslA7p43HCsnwooXTEc3UmPmCNn5lrqTJxy6nRmcavGZVt/3Da2pD5NHvsOHJCrdc1G2r3DITpU7yic7w/7Rxnjc0kt5GC4djiv2Sz3Fb2iEZg41/ddsFDoyuYrIkmFehz0HR2thPgQqMyQYb2OtB0WxsZ3BeG3+wpRb1vzl2UYBog8FfGhttFKjtAclnZYrRo9ryG9uG/FZQU4AEg8ZE9LjGMzTmqKXPLnlWVnIlQQTvxJf8ip7VgjZjyVPrjw1te5otM7RmP7xm+sK2Gv9I8Gi++BRbEkR9EBw8zRUcKxwp73xkaLiqQb+kGduJTNHG72zcW9LoJgqQxpP3/Tj//c3yB0tqzaml05/+orHLksVO+95kX7/7qgJvnjlrfr2Ggsyx0eoy9uPzN5SPd86aXggOsEKW2Prz7du3VID3/tzs/sSRs2w7ovVHKtjrX2pd7ZMlTxAYfBAL9jiDwfLkq55Tm7ifhMlTGPyCAs7RFRhn47JnlcB9RM5T97ASuZXIcVNuUDIndpDbdsfrqsOppeXl5Y+XVKdjFCTh+zGaVuj0d9zy05PPK3QzBamxdwtTCrzyg/2Rvf2EstUjordGwa/kx9mSJLr8mLLtCW8HHGJc2R5hS219IiF6PnTusOqcMl57gm0Z8kanKMAQg0qSyuZfn7zItsbGyO9QlnxY0eCuD1XL2ys/MsrQhltE7Ug0uFOzufJFE2PxBo/YAx8XPPdDwWN0MrDRYIZF0mSMKCNHgaIVFoBbNoLJ7tEQDKxGF0kcLQimojCZopv0OkNOyWCCg9XMVAi7ARJzQdM2QUh0gmBozjc3Skg6dSBRqDGYSUOu66Zg+I2fNZs/M3/f/Grl/XnyF1Gw3VKCez0PN5IUfFLqvgUN4C0qNqYs5YhPL+aVZYDE4IpUk57oSFnJm4FyCqqOE0jhY2SMyLFoo56zyo6becOS5UVDdj7Vih0zp+tcMhwRpBeLyqtIjlJKAIZSbI8SGSF3k0pA3mR5tHuwPFoa7N7reoq2bqCsAk1HqCu5uvI1n6JuRXI+S1Mco54YmYTwcn6Aeic+kssXi8XpXC4V3t7/ADuTNKaQJdScAAAAAElFTkSuQmCC)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_wf_md_setup.ipynb)
+[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb)
 
 # Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
 
@@ -35,7 +35,7 @@ git clone https://github.com/bioexcel/biobb_wf_md_setup.git
 cd biobb_wf_md_setup
 conda env create -f conda_env/environment.yml
 conda activate biobb_wf_md_setup
-jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
+jupyter-notebook biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
 ```
 
 ***
@@ -44,9 +44,9 @@ jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
 
 Click here to [view tutorial in Read the Docs](https://biobb-wf-md-setup.readthedocs.io/en/latest/tutorial.html)
 
-Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb)
+Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_wf_md_setup.ipynb)
 
-Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb)
+Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb)
 
 ***
 
diff --git a/biobb_wf_md_setup/docs/source/readme.md b/biobb_wf_md_setup/docs/source/readme.md
index 5fd4685..01e0864 100644
--- a/biobb_wf_md_setup/docs/source/readme.md
+++ b/biobb_wf_md_setup/docs/source/readme.md
@@ -1,6 +1,6 @@
 [![](https://readthedocs.org/projects/biobb-wf-md-setup/badge/?version=latest)](https://biobb-wf-md-setup.readthedocs.io/en/latest/?badge=latest)
-[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb)
-[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb)
+[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_wf_md_setup.ipynb)
+[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb)
 
 # Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
 
@@ -35,7 +35,7 @@ git clone https://github.com/bioexcel/biobb_wf_md_setup.git
 cd biobb_wf_md_setup
 conda env create -f conda_env/environment.yml
 conda activate biobb_wf_md_setup
-jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
+jupyter-notebook biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
 ```
 
 ***
@@ -44,9 +44,9 @@ jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
 
 Click here to [view tutorial in Read the Docs](https://biobb-wf-md-setup.readthedocs.io/en/latest/tutorial.html)
 
-Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb)
+Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_md_setup/HEAD?labpath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_wf_md_setup.ipynb)
 
-Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb)
+Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_md_setup/blob/main/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb)
 
 ***
 
diff --git a/biobb_wf_md_setup/docs/source/tutorial.md b/biobb_wf_md_setup/docs/source/tutorial.md
index d04ce59..440bd29 100644
--- a/biobb_wf_md_setup/docs/source/tutorial.md
+++ b/biobb_wf_md_setup/docs/source/tutorial.md
@@ -27,7 +27,7 @@ git clone https://github.com/bioexcel/biobb_wf_md_setup.git
 cd biobb_wf_md_setup
 conda env create -f conda_env/environment.yml
 conda activate biobb_wf_md_setup
-jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
+jupyter-notebook biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
 ```
 
 ***
diff --git a/biobb_wf_md_setup/html/biobb_wf_md_setup.web.html b/biobb_wf_md_setup/html/biobb_wf_md_setup.web.html
index 7869708..d9205c1 100644
--- a/biobb_wf_md_setup/html/biobb_wf_md_setup.web.html
+++ b/biobb_wf_md_setup/html/biobb_wf_md_setup.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_MDsetup_tutorial.web</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
+<title>biobb_wf_md_setup.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; }
@@ -7536,7 +7536,7 @@ <h3 id="Conda-Installation-and-Launch">Conda Installation and Launch<a class="an
 <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_md_setup</span>
-<span class="go">jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb</span>
+<span class="go">jupyter-notebook biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb</span>
 </pre></div>
 <hr/>
 <h2 id="Pipeline-steps">Pipeline steps<a class="anchor-link" href="#Pipeline-steps">¶</a></h2><ol>
diff --git a/biobb_wf_md_setup/html/biobb_wf_md_setup.web.ipynb b/biobb_wf_md_setup/html/biobb_wf_md_setup.web.ipynb
deleted file mode 100644
index 895e4fd..0000000
--- a/biobb_wf_md_setup/html/biobb_wf_md_setup.web.ipynb
+++ /dev/null
@@ -1,1541 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Protein MD Setup tutorial using BioExcel Building Blocks (biobb)\n",
-    "**Based on the official GROMACS tutorial:** [http://www.mdtutorials.com/gmx/lysozyme/index.html](http://www.mdtutorials.com/gmx/lysozyme/index.html)\n",
-    "***\n",
-    "This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI, [https://doi.org/10.2210/pdb1AKI/pdb](https://doi.org/10.2210/pdb1AKI/pdb)). \n",
-    "***\n",
-    "\n",
-    "## Settings\n",
-    "\n",
-    "### Biobb modules used\n",
-    "\n",
-    " - [biobb_io](https://github.com/bioexcel/biobb_io): Tools to fetch biomolecular data from public databases.\n",
-    " - [biobb_model](https://github.com/bioexcel/biobb_model): Tools to model macromolecular structures.\n",
-    " - [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations.\n",
-    " - [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories.\n",
-    " \n",
-    "### Auxiliary libraries used\n",
-    "\n",
-    "* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.\n",
-    "* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
-    "* [plotly](https://plot.ly/python/offline/): Python interactive graphing library integrated in Jupyter notebooks.\n",
-    "* [simpletraj](https://github.com/arose/simpletraj): Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.\n",
-    "\n",
-    "### Conda Installation and Launch\n",
-    "\n",
-    "```console\n",
-    "git clone https://github.com/bioexcel/biobb_wf_md_setup.git\n",
-    "cd biobb_wf_md_setup\n",
-    "conda env create -f conda_env/environment.yml\n",
-    "conda activate biobb_GMX_MDsetup_tutorial\n",
-    "jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb\n",
-    "```\n",
-    "\n",
-    "***\n",
-    "## Pipeline steps\n",
-    " 1. [Input Parameters](#input)\n",
-    " 2. [Fetching PDB Structure](#fetch)\n",
-    " 3. [Fix Protein Structure](#fix)\n",
-    " 4. [Create Protein System Topology](#top)\n",
-    " 5. [Create Solvent Box](#box)\n",
-    " 6. [Fill the Box with Water Molecules](#water)\n",
-    " 7. [Adding Ions](#ions)\n",
-    " 8. [Energetically Minimize the System](#min)\n",
-    " 9. [Equilibrate the System (NVT)](#nvt)\n",
-    " 10. [Equilibrate the System (NPT)](#npt)\n",
-    " 11. [Free Molecular Dynamics Simulation](#free)\n",
-    " 12. [Post-processing and Visualizing Resulting 3D Trajectory](#post)\n",
-    " 13. [Output Files](#output)\n",
-    " 14. [Questions & Comments](#questions)\n",
-    " \n",
-    "***\n",
-    "<img src=\"https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png\" alt=\"Bioexcel2 logo\"\n",
-    "\ttitle=\"Bioexcel2 logo\" width=\"400\" />\n",
-    "***\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "jp-MarkdownHeadingCollapsed": true
-   },
-   "source": [
-    "## Initializing colab\n",
-    "The two cells below are used only in case this notebook is executed via **Google Colab**. Take into account that, for running conda on **Google Colab**, the **condacolab** library must be installed. As [explained here](https://pypi.org/project/condacolab/), the installation requires a **kernel restart**, so when running this notebook in **Google Colab**, don't run all cells until this **installation** is properly **finished** and the **kernel** has **restarted**."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Only executed when using google colab\n",
-    "import sys\n",
-    "if 'google.colab' in sys.modules:\n",
-    "  import subprocess\n",
-    "  from pathlib import Path\n",
-    "  try:\n",
-    "    subprocess.run([\"conda\", \"-V\"], check=True)\n",
-    "  except FileNotFoundError:\n",
-    "    subprocess.run([sys.executable, \"-m\", \"pip\", \"install\", \"condacolab\"], check=True)\n",
-    "    import condacolab\n",
-    "    condacolab.install()\n",
-    "    # Clone repository\n",
-    "    repo_URL = \"https://github.com/bioexcel/biobb_wf_md_setup.git\"\n",
-    "    repo_name = Path(repo_URL).name.split('.')[0]\n",
-    "    if not Path(repo_name).exists():\n",
-    "      subprocess.run([\"mamba\", \"install\", \"-y\", \"git\"], check=True)\n",
-    "      subprocess.run([\"git\", \"clone\", repo_URL], check=True)\n",
-    "      print(\"⏬ Repository properly cloned.\")\n",
-    "    # Install environment\n",
-    "    print(\"⏳ Creating environment...\")\n",
-    "    env_file_path = f\"{repo_name}/conda_env/environment.yml\"\n",
-    "    subprocess.run([\"mamba\", \"env\", \"update\", \"-n\", \"base\", \"-f\", env_file_path], check=True)\n",
-    "    print(\"🎨 Install NGLView dependencies...\")\n",
-    "    subprocess.run([\"mamba\", \"install\", \"-y\", \"-c\", \"conda-forge\", \"nglview==3.0.8\", \"ipywidgets=7.7.2\"], check=True)\n",
-    "    print(\"👍 Conda environment successfully created and updated.\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Enable widgets for colab\n",
-    "if 'google.colab' in sys.modules:\n",
-    "  from google.colab import output\n",
-    "  output.enable_custom_widget_manager()\n",
-    "  # Change working dir\n",
-    "  import os\n",
-    "  os.chdir(\"biobb_wf_md_setup/biobb_wf_md_setup/notebooks\")\n",
-    "  print(f\"📂 New working directory: {os.getcwd()}\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"input\"></a>\n",
-    "## Input parameters\n",
-    "**Input parameters** needed:\n",
-    " - **pdbCode**: PDB code of the protein structure (e.g. 1AKI, [https://doi.org/10.2210/pdb1AKI/pdb](https://doi.org/10.2210/pdb1AKI/pdb))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import nglview\n",
-    "import ipywidgets\n",
-    "\n",
-    "pdbCode = \"1AKI\""
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"fetch\"></a>\n",
-    "***\n",
-    "## Fetching PDB structure\n",
-    "Downloading **PDB structure** with the **protein molecule** from the RCSB PDB database.<br>\n",
-    "Alternatively, a **PDB file** can be used as starting structure. <br>\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Pdb](https://biobb-io.readthedocs.io/en/latest/api.html#module-api.pdb) from **biobb_io.api.pdb**\n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Downloading desired PDB file \n",
-    "# Import module\n",
-    "from biobb_io.api.pdb import pdb\n",
-    "\n",
-    "# Create properties dict and inputs/outputs\n",
-    "downloaded_pdb = pdbCode+'.pdb'\n",
-    "prop = {\n",
-    "    'pdb_code': pdbCode\n",
-    "}\n",
-    "\n",
-    "#Create and launch bb\n",
-    "pdb(output_pdb_path=downloaded_pdb,\n",
-    "    properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"vis3D\"></a>\n",
-    "### Visualizing 3D structure\n",
-    "Visualizing the downloaded/given **PDB structure** using **NGL**:    "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# Show protein\n",
-    "view = nglview.show_structure_file(downloaded_pdb)\n",
-    "view.add_representation(repr_type='ball+stick', selection='all')\n",
-    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
-    "view"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='ngl1.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"fix\"></a>\n",
-    "***\n",
-    "## Fix protein structure\n",
-    "**Checking** and **fixing** (if needed) the protein structure:<br>\n",
-    "- **Modeling** **missing side-chain atoms**, modifying incorrect **amide assignments**, choosing **alternative locations**.<br>\n",
-    "- **Checking** for missing **backbone atoms**, **heteroatoms**, **modified residues** and possible **atomic clashes**.\n",
-    "\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [FixSideChain](https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain) from **biobb_model.model.fix_side_chain**\n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Check & Fix PDB\n",
-    "# Import module\n",
-    "from biobb_model.model.fix_side_chain import fix_side_chain\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "fixed_pdb = pdbCode + '_fixed.pdb'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "fix_side_chain(input_pdb_path=downloaded_pdb, \n",
-    "             output_pdb_path=fixed_pdb)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Visualizing 3D structure\n",
-    "Visualizing the fixed **PDB structure** using **NGL**. 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.   "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# Show protein\n",
-    "view = nglview.show_structure_file(fixed_pdb)\n",
-    "view.add_representation(repr_type='ball+stick', selection='all')\n",
-    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
-    "view.camera='orthographic'\n",
-    "view"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='ngl2.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"top\"></a>\n",
-    "***\n",
-    "## Create protein system topology\n",
-    "**Building GROMACS topology** corresponding to the protein structure.<br>\n",
-    "Force field used in this tutorial is [**amber99sb-ildn**](https://dx.doi.org/10.1002%2Fprot.22711): AMBER **parm99** force field with **corrections on backbone** (sb) and **side-chain torsion potentials** (ildn). Water molecules type used in this tutorial is [**spc/e**](https://pubs.acs.org/doi/abs/10.1021/j100308a038).<br>\n",
-    "Adding **hydrogen atoms** if missing. Automatically identifying **disulfide bridges**. <br>\n",
-    "\n",
-    "Generating two output files: \n",
-    "- **GROMACS structure** (gro file)\n",
-    "- **GROMACS topology** ZIP compressed file containing:\n",
-    "    - *GROMACS topology top file* (top file)\n",
-    "    - *GROMACS position restraint file/s* (itp file/s)\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Pdb2gmx](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.pdb2gmx) from **biobb_gromacs.gromacs.pdb2gmx**\n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Create system topology\n",
-    "# Import module\n",
-    "from biobb_gromacs.gromacs.pdb2gmx import pdb2gmx\n",
-    "\n",
-    "# Create inputs/outputs\n",
-    "output_pdb2gmx_gro = pdbCode+'_pdb2gmx.gro'\n",
-    "output_pdb2gmx_top_zip = pdbCode+'_pdb2gmx_top.zip'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "pdb2gmx(input_pdb_path=fixed_pdb, \n",
-    "        output_gro_path=output_pdb2gmx_gro, \n",
-    "        output_top_zip_path=output_pdb2gmx_top_zip)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Visualizing 3D structure\n",
-    "Visualizing the generated **GRO structure** using **NGL**. Note that **hydrogen atoms** were added to the structure by the **pdb2gmx GROMACS tool** when generating the **topology**.    "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# Show protein\n",
-    "view = nglview.show_structure_file(output_pdb2gmx_gro)\n",
-    "view.add_representation(repr_type='ball+stick', selection='all')\n",
-    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
-    "view.camera='orthographic'\n",
-    "view"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='ngl3.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"box\"></a>\n",
-    "***\n",
-    "## Create solvent box\n",
-    "Define the unit cell for the **protein structure MD system** to fill it with water molecules.<br>\n",
-    "A **cubic box** is used to define the unit cell, with a **distance from the protein to the box edge of 1.0 nm**. The protein is **centered in the box**.  \n",
-    "\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Editconf](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.editconf) from **biobb_gromacs.gromacs.editconf** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Editconf: Create solvent box\n",
-    "# Import module\n",
-    "from biobb_gromacs.gromacs.editconf import editconf\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_editconf_gro = pdbCode+'_editconf.gro'\n",
-    "\n",
-    "prop = {\n",
-    "    'box_type': 'cubic',\n",
-    "    'distance_to_molecule': 1.0\n",
-    "}\n",
-    "\n",
-    "#Create and launch bb\n",
-    "editconf(input_gro_path=output_pdb2gmx_gro, \n",
-    "         output_gro_path=output_editconf_gro,\n",
-    "         properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"water\"></a>\n",
-    "***\n",
-    "## Fill the box with water molecules\n",
-    "Fill the unit cell for the **protein structure system** with water molecules.<br>\n",
-    "The solvent type used is the default **Simple Point Charge water (SPC)**, a generic equilibrated 3-point solvent model. \n",
-    "\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Solvate](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.solvate) from **biobb_gromacs.gromacs.solvate** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Solvate: Fill the box with water molecules\n",
-    "from biobb_gromacs.gromacs.solvate import solvate\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_solvate_gro = pdbCode+'_solvate.gro'\n",
-    "output_solvate_top_zip = pdbCode+'_solvate_top.zip'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "solvate(input_solute_gro_path=output_editconf_gro, \n",
-    "        output_gro_path=output_solvate_gro, \n",
-    "        input_top_zip_path=output_pdb2gmx_top_zip, \n",
-    "        output_top_zip_path=output_solvate_top_zip)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Visualizing 3D structure\n",
-    "Visualizing the **protein system** with the newly added **solvent box** using **NGL**.<br> Note the **cubic box** filled with **water molecules** surrounding the **protein structure**, which is **centered** right in the middle of the cube."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# Show protein\n",
-    "view = nglview.show_structure_file(output_solvate_gro)\n",
-    "view.clear_representations()\n",
-    "view.add_representation(repr_type='cartoon', selection='solute', color='green')\n",
-    "view.add_representation(repr_type='ball+stick', selection='SOL')\n",
-    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
-    "view.camera='orthographic'\n",
-    "view"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='ngl4.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"ions\"></a>\n",
-    "***\n",
-    "## Adding ions\n",
-    "Add ions to neutralize the **protein structure** charge\n",
-    "- [Step 1](#ionsStep1): Creating portable binary run file for ion generation\n",
-    "- [Step 2](#ionsStep2): Adding ions to **neutralize** the system\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Grompp](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp) from **biobb_gromacs.gromacs.grompp** \n",
-    " - [Genion](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genion) from **biobb_gromacs.gromacs.genion** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"ionsStep1\"></a>\n",
-    "### Step 1: Creating portable binary run file for ion generation\n",
-    "A simple **energy minimization** molecular dynamics parameters (mdp) properties will be used to generate the portable binary run file for **ion generation**, although **any legitimate combination of parameters** could be used in this step."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Grompp: Creating portable binary run file for ion generation\n",
-    "from biobb_gromacs.gromacs.grompp import grompp\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_gppion_tpr = pdbCode+'_gppion.tpr'\n",
-    "prop = {\n",
-    "    'simulation_type': 'minimization',\n",
-    "    'maxwarn': 1\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "grompp(input_gro_path=output_solvate_gro, \n",
-    "       input_top_zip_path=output_solvate_top_zip, \n",
-    "       output_tpr_path=output_gppion_tpr,  \n",
-    "       properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"ionsStep2\"></a>\n",
-    "### Step 2: Adding ions to neutralize the system\n",
-    "Replace **solvent molecules** with **ions** to **neutralize** the system."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Genion: Adding ions to neutralize the system\n",
-    "from biobb_gromacs.gromacs.genion import genion\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_genion_gro = pdbCode+'_genion.gro'\n",
-    "output_genion_top_zip = pdbCode+'_genion_top.zip'\n",
-    "prop={\n",
-    "    'neutral':True\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "genion(input_tpr_path=output_gppion_tpr, \n",
-    "       output_gro_path=output_genion_gro, \n",
-    "       input_top_zip_path=output_solvate_top_zip, \n",
-    "       output_top_zip_path=output_genion_top_zip, \n",
-    "       properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Visualizing 3D structure\n",
-    "Visualizing the **neutralized protein system** with the newly added **ions** using **NGL**"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# Show protein\n",
-    "view = nglview.show_structure_file(output_genion_gro)\n",
-    "view.clear_representations()\n",
-    "view.add_representation(repr_type='cartoon', selection='solute', color='sstruc')\n",
-    "view.add_representation(repr_type='ball+stick', selection='NA')\n",
-    "view.add_representation(repr_type='ball+stick', selection='CL')\n",
-    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
-    "view.camera='orthographic'\n",
-    "view"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='ngl5.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"min\"></a>\n",
-    "***\n",
-    "## Energetically minimize the system\n",
-    "Energetically minimize the **protein system** till reaching a desired potential energy.\n",
-    "- [Step 1](#emStep1): Creating portable binary run file for energy minimization\n",
-    "- [Step 2](#emStep2): Energetically minimize the **system** till reaching a force of 500 kJ/mol*nm.\n",
-    "- [Step 3](#emStep3): Checking **energy minimization** results. Plotting energy by time during the **minimization** process.\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Grompp](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp) from **biobb_gromacs.gromacs.grompp** \n",
-    " - [Mdrun](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun) from **biobb_gromacs.gromacs.mdrun** \n",
-    " - [GMXEnergy](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy) from **biobb_analysis.gromacs.gmx_energy** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"emStep1\"></a>\n",
-    "### Step 1: Creating portable binary run file for energy minimization\n",
-    "The **minimization** type of the **molecular dynamics parameters (mdp) property** contains the main default parameters to run an **energy minimization**:\n",
-    "\n",
-    "-  integrator  = steep ; Algorithm (steep = steepest descent minimization)\n",
-    "-  emtol       = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm\n",
-    "-  emstep      = 0.01 ; Minimization step size (nm)\n",
-    "-  nsteps      = 50000 ; Maximum number of (minimization) steps to perform\n",
-    "\n",
-    "In this particular example, the method used to run the **energy minimization** is the default **steepest descent**, but the **maximum force** is placed at **500 kJ/mol\\*nm^2**, and the **maximum number of steps** to perform (if the maximum force is not reached) to **5,000 steps**. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Grompp: Creating portable binary run file for mdrun\n",
-    "from biobb_gromacs.gromacs.grompp import grompp\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_gppmin_tpr = pdbCode+'_gppmin.tpr'\n",
-    "prop = {\n",
-    "    'mdp':{\n",
-    "        'emtol':'500',\n",
-    "        'nsteps':'5000'\n",
-    "    },\n",
-    "    'simulation_type': 'minimization'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "grompp(input_gro_path=output_genion_gro, \n",
-    "       input_top_zip_path=output_genion_top_zip, \n",
-    "       output_tpr_path=output_gppmin_tpr,  \n",
-    "       properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"emStep2\"></a>\n",
-    "### Step 2: Running Energy Minimization\n",
-    "Running **energy minimization** using the **tpr file** generated in the previous step. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Mdrun: Running minimization\n",
-    "from biobb_gromacs.gromacs.mdrun import mdrun\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_min_trr = pdbCode+'_min.trr'\n",
-    "output_min_gro = pdbCode+'_min.gro'\n",
-    "output_min_edr = pdbCode+'_min.edr'\n",
-    "output_min_log = pdbCode+'_min.log'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "mdrun(input_tpr_path=output_gppmin_tpr, \n",
-    "      output_trr_path=output_min_trr, \n",
-    "      output_gro_path=output_min_gro, \n",
-    "      output_edr_path=output_min_edr, \n",
-    "      output_log_path=output_min_log)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"emStep3\"></a>\n",
-    "### Step 3: Checking Energy Minimization results\n",
-    "Checking **energy minimization** results. Plotting **potential energy** by time during the minimization process. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXEnergy: Getting system energy by time  \n",
-    "from biobb_analysis.gromacs.gmx_energy import gmx_energy\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_min_ene_xvg = pdbCode+'_min_ene.xvg'\n",
-    "prop = {\n",
-    "    'terms':  [\"Potential\"]\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_energy(input_energy_path=output_min_edr, \n",
-    "          output_xvg_path=output_min_ene_xvg, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import plotly.graph_objs as go\n",
-    "\n",
-    "# Read data from file and filter energy values higher than 1000 kJ/mol\n",
-    "with open(output_min_ene_xvg, 'r') as energy_file:\n",
-    "    x, y = zip(*[\n",
-    "        (float(line.split()[0]), float(line.split()[1]))\n",
-    "        for line in energy_file\n",
-    "        if not line.startswith((\"#\", \"@\"))\n",
-    "        if float(line.split()[1]) < 1000\n",
-    "    ])\n",
-    "\n",
-    "# Create a scatter plot\n",
-    "fig = go.Figure(data=go.Scatter(x=x, y=y, mode='lines'))\n",
-    "\n",
-    "# Update layout\n",
-    "fig.update_layout(title=\"Energy Minimization\",\n",
-    "                  xaxis_title=\"Energy Minimization Step\",\n",
-    "                  yaxis_title=\"Potential Energy kJ/mol\",\n",
-    "                  height=600)\n",
-    "\n",
-    "# Show the figure (renderer changes for colab and jupyter)\n",
-    "rend = 'colab' if 'google.colab' in sys.modules else ''\n",
-    "fig.show(renderer=rend)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='plot1.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"nvt\"></a>\n",
-    "***\n",
-    "## Equilibrate the system (NVT)\n",
-    "Equilibrate the **protein system** in **NVT ensemble** (constant Number of particles, Volume and Temperature). Protein **heavy atoms** 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.\n",
-    "\n",
-    "- [Step 1](#eqNVTStep1): Creating portable binary run file for system equilibration\n",
-    "- [Step 2](#eqNVTStep2): Equilibrate the **protein system** with **NVT** ensemble.\n",
-    "- [Step 3](#eqNVTStep3): Checking **NVT Equilibration** results. Plotting **system temperature** by time during the **NVT equilibration** process. \n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    "- [Grompp](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp) from **biobb_gromacs.gromacs.grompp** \n",
-    "- [Mdrun](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun) from **biobb_gromacs.gromacs.mdrun** \n",
-    "- [GMXEnergy](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy) from **biobb_analysis.gromacs.gmx_energy** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"eqNVTStep1\"></a>\n",
-    "### Step 1: Creating portable binary run file for system equilibration (NVT)\n",
-    "The **nvt** type of the **molecular dynamics parameters (mdp) property** contains the main default parameters to run an **NVT equilibration** with **protein restraints** (see [GROMACS mdp options](http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html)):\n",
-    "\n",
-    "-  Define                   = -DPOSRES\n",
-    "-  integrator               = md\n",
-    "-  dt                       = 0.002\n",
-    "-  nsteps                   = 5000\n",
-    "-  pcoupl                   = no\n",
-    "-  gen_vel                  = yes\n",
-    "-  gen_temp                 = 300\n",
-    "-  gen_seed                 = -1\n",
-    "\n",
-    "In this particular example, the default parameters will be used: **md** integrator algorithm, a **step size** of **2fs**, **5,000 equilibration steps** with the protein **heavy atoms restrained**, and a temperature of **300K**.\n",
-    "\n",
-    "*Please note that for the sake of time this tutorial is only running 10ps of NVT equilibration, whereas in the [original example](http://www.mdtutorials.com/gmx/lysozyme/06_equil.html) the simulated time was 100ps.*"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Grompp: Creating portable binary run file for NVT Equilibration\n",
-    "from biobb_gromacs.gromacs.grompp import grompp\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_gppnvt_tpr = pdbCode+'_gppnvt.tpr'\n",
-    "prop = {\n",
-    "    'mdp':{\n",
-    "        'nsteps': 5000,\n",
-    "        'dt': 0.002,\n",
-    "        'Define': '-DPOSRES',\n",
-    "        #'tc_grps': \"DNA Water_and_ions\" # NOTE: uncomment this line if working with DNA\n",
-    "    },\n",
-    "    'simulation_type': 'nvt'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "grompp(input_gro_path=output_min_gro, \n",
-    "       input_top_zip_path=output_genion_top_zip, \n",
-    "       output_tpr_path=output_gppnvt_tpr,  \n",
-    "       properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"eqNVTStep2\"></a>\n",
-    "### Step 2: Running NVT equilibration"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Mdrun: Running Equilibration NVT\n",
-    "from biobb_gromacs.gromacs.mdrun import mdrun\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_nvt_trr = pdbCode+'_nvt.trr'\n",
-    "output_nvt_gro = pdbCode+'_nvt.gro'\n",
-    "output_nvt_edr = pdbCode+'_nvt.edr'\n",
-    "output_nvt_log = pdbCode+'_nvt.log'\n",
-    "output_nvt_cpt = pdbCode+'_nvt.cpt'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "mdrun(input_tpr_path=output_gppnvt_tpr, \n",
-    "      output_trr_path=output_nvt_trr, \n",
-    "      output_gro_path=output_nvt_gro, \n",
-    "      output_edr_path=output_nvt_edr, \n",
-    "      output_log_path=output_nvt_log, \n",
-    "      output_cpt_path=output_nvt_cpt)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"eqNVTStep3\"></a>\n",
-    "### Step 3: Checking NVT Equilibration results\n",
-    "Checking **NVT Equilibration** results. Plotting **system temperature** by time during the NVT equilibration process. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXEnergy: Getting system temperature by time during NVT Equilibration  \n",
-    "from biobb_analysis.gromacs.gmx_energy import gmx_energy\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_nvt_temp_xvg = pdbCode+'_nvt_temp.xvg'\n",
-    "prop = {\n",
-    "    'terms':  [\"Temperature\"]\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_energy(input_energy_path=output_nvt_edr, \n",
-    "          output_xvg_path=output_nvt_temp_xvg, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import plotly.graph_objs as go\n",
-    "\n",
-    "# Read temperature data from file\n",
-    "with open(output_nvt_temp_xvg, 'r') as temperature_file:\n",
-    "    x, y = zip(*[\n",
-    "        (float(line.split()[0]), float(line.split()[1]))\n",
-    "        for line in temperature_file\n",
-    "        if not line.startswith((\"#\", \"@\"))\n",
-    "    ])\n",
-    "\n",
-    "# Create a scatter plot\n",
-    "fig = go.Figure(data=go.Scatter(x=x, y=y, mode='lines+markers'))\n",
-    "\n",
-    "# Update layout\n",
-    "fig.update_layout(title=\"Temperature during NVT Equilibration\",\n",
-    "                  xaxis_title=\"Time (ps)\",\n",
-    "                  yaxis_title=\"Temperature (K)\",\n",
-    "                  height=600)\n",
-    "\n",
-    "# Show the figure (renderer changes for colab and jupyter)\n",
-    "rend = 'colab' if 'google.colab' in sys.modules else ''\n",
-    "fig.show(renderer=rend)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='plot2.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"npt\"></a>\n",
-    "***\n",
-    "## Equilibrate the system (NPT)\n",
-    "Equilibrate the **protein system** in **NPT** ensemble (constant Number of particles, Pressure and Temperature).\n",
-    "- [Step 1](#eqNPTStep1): Creating portable binary run file for system equilibration\n",
-    "- [Step 2](#eqNPTStep2): Equilibrate the **protein system** with **NPT** ensemble.\n",
-    "- [Step 3](#eqNPTStep3): Checking **NPT Equilibration** results. Plotting **system pressure and density** by time during the **NPT equilibration** process.\n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Grompp](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp) from **biobb_gromacs.gromacs.grompp** \n",
-    " - [Mdrun](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun) from **biobb_gromacs.gromacs.mdrun** \n",
-    " - [GMXEnergy](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy) from **biobb_analysis.gromacs.gmx_energy** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"eqNPTStep1\"></a>\n",
-    "### Step 1: Creating portable binary run file for system equilibration (NPT)\n",
-    "\n",
-    "The **npt** type of the **molecular dynamics parameters (mdp) property** contains the main default parameters to run an **NPT equilibration** with **protein restraints** (see [GROMACS mdp options](http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html)):\n",
-    "\n",
-    "-  Define                   = -DPOSRES\n",
-    "-  integrator               = md\n",
-    "-  dt                       = 0.002\n",
-    "-  nsteps                   = 5000\n",
-    "-  pcoupl = Parrinello-Rahman\n",
-    "-  pcoupltype = isotropic\n",
-    "-  tau_p = 1.0\n",
-    "-  ref_p = 1.0\n",
-    "-  compressibility = 4.5e-5\n",
-    "-  refcoord_scaling = com\n",
-    "-  gen_vel = no\n",
-    "\n",
-    "In this particular example, the default parameters will be used: **md** integrator algorithm, a **time step** of **2fs**, **5,000 equilibration steps** with the protein **heavy atoms restrained**, and a Parrinello-Rahman **pressure coupling** algorithm.\n",
-    "\n",
-    "*Please note that for the sake of time this tutorial is only running 10ps of NPT equilibration, whereas in the [original example](http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html) the simulated time was 100ps.*"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Grompp: Creating portable binary run file for NPT System Equilibration\n",
-    "from biobb_gromacs.gromacs.grompp import grompp\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_gppnpt_tpr = pdbCode+'_gppnpt.tpr'\n",
-    "prop = {\n",
-    "    'mdp':{\n",
-    "        'nsteps':'5000',\n",
-    "        #'tc_grps': \"DNA Water_and_ions\" # NOTE: uncomment this line if working with DNA\n",
-    "    },\n",
-    "    'simulation_type': 'npt'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "grompp(input_gro_path=output_nvt_gro, \n",
-    "       input_top_zip_path=output_genion_top_zip, \n",
-    "       output_tpr_path=output_gppnpt_tpr, \n",
-    "       input_cpt_path=output_nvt_cpt,  \n",
-    "       properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"eqNPTStep2\"></a>\n",
-    "### Step 2: Running NPT equilibration"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Mdrun: Running NPT System Equilibration\n",
-    "from biobb_gromacs.gromacs.mdrun import mdrun\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_npt_trr = pdbCode+'_npt.trr'\n",
-    "output_npt_gro = pdbCode+'_npt.gro'\n",
-    "output_npt_edr = pdbCode+'_npt.edr'\n",
-    "output_npt_log = pdbCode+'_npt.log'\n",
-    "output_npt_cpt = pdbCode+'_npt.cpt'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "mdrun(input_tpr_path=output_gppnpt_tpr, \n",
-    "      output_trr_path=output_npt_trr, \n",
-    "      output_gro_path=output_npt_gro, \n",
-    "      output_edr_path=output_npt_edr, \n",
-    "      output_log_path=output_npt_log, \n",
-    "      output_cpt_path=output_npt_cpt)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"eqNPTStep3\"></a>\n",
-    "### Step 3: Checking NPT Equilibration results\n",
-    "Checking **NPT Equilibration** results. Plotting **system pressure and density** by time during the **NPT equilibration** process. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXEnergy: Getting system pressure and density by time during NPT Equilibration  \n",
-    "from biobb_analysis.gromacs.gmx_energy import gmx_energy\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_npt_pd_xvg = pdbCode+'_npt_PD.xvg'\n",
-    "prop = {\n",
-    "    'terms':  [\"Pressure\",\"Density\"]\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_energy(input_energy_path=output_npt_edr, \n",
-    "          output_xvg_path=output_npt_pd_xvg, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import plotly.graph_objs as go\n",
-    "from plotly.subplots import make_subplots\n",
-    "\n",
-    "# Read pressure and density data from file \n",
-    "with open(output_npt_pd_xvg,'r') as pd_file:\n",
-    "    x, y, z = zip(*[\n",
-    "        (float(line.split()[0]), float(line.split()[1]), float(line.split()[2]))\n",
-    "        for line in pd_file\n",
-    "        if not line.startswith((\"#\", \"@\"))\n",
-    "    ])\n",
-    "\n",
-    "trace1 = go.Scatter(\n",
-    "    x=x,y=y\n",
-    ")\n",
-    "trace2 = go.Scatter(\n",
-    "    x=x,y=z\n",
-    ")\n",
-    "\n",
-    "fig = make_subplots(rows=1, cols=2, print_grid=False)\n",
-    "fig.append_trace(trace1, 1, 1)\n",
-    "fig.append_trace(trace2, 1, 2)\n",
-    "\n",
-    "fig.update_layout(\n",
-    "    height=500,\n",
-    "    title='Pressure and Density during NPT Equilibration',\n",
-    "    showlegend=False,\n",
-    "    xaxis1_title='Time (ps)',\n",
-    "    yaxis1_title='Pressure (bar)',\n",
-    "    xaxis2_title='Time (ps)',\n",
-    "    yaxis2_title='Density (Kg*m^-3)'\n",
-    ")\n",
-    "\n",
-    "# Show the figure (renderer changes for colab and jupyter)\n",
-    "rend = 'colab' if 'google.colab' in sys.modules else ''\n",
-    "fig.show(renderer=rend)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='plot3.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"free\"></a>\n",
-    "***\n",
-    "## Free Molecular Dynamics Simulation\n",
-    "Upon completion of the **two equilibration phases (NVT and NPT)**, the system is now well-equilibrated at the desired temperature and pressure. The **position restraints** can now be released. The last step of the **protein** MD setup is a short, **free MD simulation**, to ensure the robustness of the system. \n",
-    "- [Step 1](#mdStep1): Creating portable binary run file to run a **free MD simulation**.\n",
-    "- [Step 2](#mdStep2): Run short MD simulation of the **protein system**.\n",
-    "- [Step 3](#mdStep3): Checking results for the final step of the setup process, the **free MD run**. Plotting **Root Mean Square deviation (RMSd)** and **Radius of Gyration (Rgyr)** by time during the **free MD run** step. \n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [Grompp](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp) from **biobb_gromacs.gromacs.grompp** \n",
-    " - [Mdrun](https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun) from **biobb_gromacs.gromacs.mdrun** \n",
-    " - [GMXRms](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_rms) from **biobb_analysis.gromacs.gmx_rms** \n",
-    " - [GMXRgyr](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_rgyr) from **biobb_analysis.gromacs.gmx_rgyr** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"mdStep1\"></a>\n",
-    "### Step 1: Creating portable binary run file to run a free MD simulation\n",
-    "\n",
-    "The **free** type of the **molecular dynamics parameters (mdp) property** contains the main default parameters to run an **free MD simulation** (see [GROMACS mdp options](http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html)):\n",
-    "\n",
-    "-  integrator               = md\n",
-    "-  dt                       = 0.002 (ps)\n",
-    "-  nsteps                   = 50000\n",
-    "\n",
-    "In this particular example, the default parameters will be used: **md** integrator algorithm, a **time step** of **2fs**, and a total of **50,000 md steps** (100ps).\n",
-    "\n",
-    "*Please note that for the sake of time this tutorial is only running 100ps of free MD, whereas in the [original example](http://www.mdtutorials.com/gmx/lysozyme/08_MD.html) the simulated time was 1ns (1000ps).*"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Grompp: Creating portable binary run file for mdrun\n",
-    "from biobb_gromacs.gromacs.grompp import grompp\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_gppmd_tpr = pdbCode+'_gppmd.tpr'\n",
-    "prop = {\n",
-    "    'mdp':{\n",
-    "        'nsteps':'50000',\n",
-    "        #'tc_grps': \"DNA Water_and_ions\" # NOTE: uncomment this line if working with DNA\n",
-    "    },\n",
-    "    'simulation_type': 'free'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "grompp(input_gro_path=output_npt_gro, \n",
-    "       input_top_zip_path=output_genion_top_zip, \n",
-    "       output_tpr_path=output_gppmd_tpr, \n",
-    "       input_cpt_path=output_npt_cpt, \n",
-    "       properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"mdStep2\"></a>\n",
-    "### Step 2: Running short free MD simulation"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Mdrun: Running free dynamics\n",
-    "from biobb_gromacs.gromacs.mdrun import mdrun\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_md_trr = pdbCode+'_md.trr'\n",
-    "output_md_gro = pdbCode+'_md.gro'\n",
-    "output_md_edr = pdbCode+'_md.edr'\n",
-    "output_md_log = pdbCode+'_md.log'\n",
-    "output_md_cpt = pdbCode+'_md.cpt'\n",
-    "\n",
-    "# Create and launch bb\n",
-    "mdrun(input_tpr_path=output_gppmd_tpr, \n",
-    "      output_trr_path=output_md_trr, \n",
-    "      output_gro_path=output_md_gro, \n",
-    "      output_edr_path=output_md_edr, \n",
-    "      output_log_path=output_md_log, \n",
-    "      output_cpt_path=output_md_cpt)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"mdStep3\"></a>\n",
-    "### Step 3: Checking free MD simulation results\n",
-    "Checking results for the final step of the setup process, the **free MD run**. Plotting **Root Mean Square deviation (RMSd)** and **Radius of Gyration (Rgyr)** by time during the **free MD run** step. **RMSd** against the **experimental structure** (input structure of the pipeline) and against the **minimized and equilibrated structure** (output structure of the NPT equilibration step)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXRms: Computing Root Mean Square deviation to analyse structural stability \n",
-    "#         RMSd against minimized and equilibrated snapshot (backbone atoms)   \n",
-    "\n",
-    "from biobb_analysis.gromacs.gmx_rms import gmx_rms\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_rms_first = pdbCode+'_rms_first.xvg'\n",
-    "prop = {\n",
-    "    'selection':  'Backbone',\n",
-    "    #'selection': 'non-Water'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_rms(input_structure_path=output_gppmd_tpr,\n",
-    "         input_traj_path=output_md_trr,\n",
-    "         output_xvg_path=output_rms_first, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXRms: Computing Root Mean Square deviation to analyse structural stability \n",
-    "#         RMSd against experimental structure (backbone atoms)   \n",
-    "\n",
-    "from biobb_analysis.gromacs.gmx_rms import gmx_rms\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_rms_exp = pdbCode+'_rms_exp.xvg'\n",
-    "prop = {\n",
-    "    'selection':  'Backbone',\n",
-    "    #'selection': 'non-Water'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_rms(input_structure_path=output_gppmin_tpr,\n",
-    "         input_traj_path=output_md_trr,\n",
-    "         output_xvg_path=output_rms_exp, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import plotly.graph_objs as go\n",
-    "\n",
-    "# Read RMS vs first snapshot data from file \n",
-    "with open(output_rms_first,'r') as rms_first_file:\n",
-    "    x, y = zip(*[\n",
-    "        (float(line.split()[0]), float(line.split()[1]))\n",
-    "        for line in rms_first_file\n",
-    "        if not line.startswith((\"#\", \"@\"))\n",
-    "    ])\n",
-    "\n",
-    "# Read RMS vs experimental structure data from file \n",
-    "with open(output_rms_exp,'r') as rms_exp_file:\n",
-    "    x2, y2 = zip(*[\n",
-    "        (float(line.split()[0]), float(line.split()[1]))\n",
-    "        for line in rms_exp_file\n",
-    "        if not line.startswith((\"#\", \"@\"))\n",
-    "    ])\n",
-    "\n",
-    "fig = make_subplots()\n",
-    "fig.add_trace(go.Scatter(x=x, y=y, mode=\"lines+markers\", name=\"RMSd vs first\"))\n",
-    "fig.add_trace(go.Scatter(x=x, y=y2, mode=\"lines+markers\", name=\"RMSd vs exp\"))\n",
-    "\n",
-    "# Set layout including height\n",
-    "fig.update_layout(\n",
-    "    title=\"RMSd during free MD Simulation\",\n",
-    "    xaxis=dict(title=\"Time (ps)\"),\n",
-    "    yaxis=dict(title=\"RMSd (nm)\"),\n",
-    "    height=600\n",
-    ")\n",
-    "\n",
-    "# Show the figure (renderer changes for colab and jupyter)\n",
-    "rend = 'colab' if 'google.colab' in sys.modules else ''\n",
-    "fig.show(renderer=rend)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='plot4.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXRgyr: Computing Radius of Gyration to measure the protein compactness during the free MD simulation \n",
-    "\n",
-    "from biobb_analysis.gromacs.gmx_rgyr import gmx_rgyr\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_rgyr = pdbCode+'_rgyr.xvg'\n",
-    "prop = {\n",
-    "    'selection':  'Backbone'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_rgyr(input_structure_path=output_gppmin_tpr,\n",
-    "         input_traj_path=output_md_trr,\n",
-    "         output_xvg_path=output_rgyr, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import plotly.graph_objs as go\n",
-    "\n",
-    "# Read Rgyr data from file\n",
-    "with open(output_rgyr, 'r') as rgyr_file:\n",
-    "    x, y = zip(*[\n",
-    "        (float(line.split()[0]), float(line.split()[1]))\n",
-    "        for line in rgyr_file\n",
-    "        if not line.startswith((\"#\", \"@\"))\n",
-    "    ])\n",
-    "\n",
-    "# Create a scatter plot\n",
-    "fig = go.Figure(data=go.Scatter(x=x, y=y, mode='lines+markers'))\n",
-    "\n",
-    "# Update layout\n",
-    "fig.update_layout(title=\"Radius of Gyration\",\n",
-    "                  xaxis_title=\"Time (ps)\",\n",
-    "                  yaxis_title=\"Rgyr (nm)\",\n",
-    "                  height=600)\n",
-    "\n",
-    "# Show the figure (renderer changes for colab and jupyter)\n",
-    "rend = 'colab' if 'google.colab' in sys.modules else ''\n",
-    "fig.show(renderer=rend)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='plot5.png'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"post\"></a>\n",
-    "***\n",
-    "## Post-processing and Visualizing resulting 3D trajectory\n",
-    "Post-processing and Visualizing the **protein system** MD setup **resulting trajectory** using **NGL**\n",
-    "- [Step 1](#ppStep1): *Imaging* the resulting trajectory, **stripping out water molecules and ions** and **correcting periodicity issues**.\n",
-    "- [Step 2](#ppStep2): Generating a *dry* structure, **removing water molecules and ions** from the final snapshot of the MD setup pipeline.\n",
-    "- [Step 3](#ppStep3): Visualizing the *imaged* trajectory using the *dry* structure as a **topology**. \n",
-    "***\n",
-    "**Building Blocks** used:\n",
-    " - [GMXImage](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_image) from **biobb_analysis.gromacs.gmx_image** \n",
-    " - [GMXTrjConvStr](https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_trjconv_str) from **biobb_analysis.gromacs.gmx_trjconv_str** \n",
-    "***"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"ppStep1\"></a>\n",
-    "### Step 1: *Imaging* the resulting trajectory.\n",
-    "Stripping out **water molecules and ions** and **correcting periodicity issues**  "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXImage: \"Imaging\" the resulting trajectory\n",
-    "#           Removing water molecules and ions from the resulting structure\n",
-    "from biobb_analysis.gromacs.gmx_image import gmx_image\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_imaged_traj = pdbCode+'_imaged_traj.trr'\n",
-    "prop = {\n",
-    "    'center_selection':  'Protein',\n",
-    "    'output_selection': 'Protein',\n",
-    "    'pbc' : 'mol',\n",
-    "    'center' : True\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_image(input_traj_path=output_md_trr,\n",
-    "         input_top_path=output_gppmd_tpr,\n",
-    "         output_traj_path=output_imaged_traj, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"ppStep2\"></a>\n",
-    "### Step 2: Generating the output *dry* structure.\n",
-    "**Removing water molecules and ions** from the resulting structure"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# GMXTrjConvStr: Converting and/or manipulating a structure\n",
-    "#                Removing water molecules and ions from the resulting structure\n",
-    "#                The \"dry\" structure will be used as a topology to visualize \n",
-    "#                the \"imaged dry\" trajectory generated in the previous step.\n",
-    "from biobb_analysis.gromacs.gmx_trjconv_str import gmx_trjconv_str\n",
-    "\n",
-    "# Create prop dict and inputs/outputs\n",
-    "output_dry_gro = pdbCode+'_md_dry.gro'\n",
-    "prop = {\n",
-    "    'selection':  'Protein'\n",
-    "}\n",
-    "\n",
-    "# Create and launch bb\n",
-    "gmx_trjconv_str(input_structure_path=output_md_gro,\n",
-    "         input_top_path=output_gppmd_tpr,\n",
-    "         output_str_path=output_dry_gro, \n",
-    "          properties=prop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a id=\"ppStep3\"></a>\n",
-    "### Step 3: Visualizing the generated dehydrated trajectory.\n",
-    "Using the **imaged trajectory** (output of the [Post-processing step 1](#ppStep1)) with the **dry structure** (output of the [Post-processing step 2](#ppStep2)) as a topology."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Show trajectory\n",
-    "view = nglview.show_simpletraj(nglview.SimpletrajTrajectory(output_imaged_traj, output_dry_gro), gui=True)\n",
-    "view"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<img src='trajectory.gif'></img>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "variables": {
-     "output_genion_top_zip": "1AKI_genion_top.zip",
-     "output_gppmd_tpr": "1AKI_gppmd.tpr",
-     "output_md_cpt": "1AKI_md.cpt",
-     "output_md_gro": "1AKI_md.gro",
-     "output_md_trr": "1AKI_md.trr",
-     "output_rgyr": "1AKI_rgyr.xvg",
-     "output_rms_exp": "1AKI_rms_exp.xvg",
-     "output_rms_first": "1AKI_rms_first.xvg"
-    }
-   },
-   "source": [
-    "<a id=\"output\"></a>\n",
-    "## Output files\n",
-    "\n",
-    "Important **Output files** generated:\n",
-    " - {{output_md_gro}}: **Final structure** (snapshot) of the MD setup protocol.\n",
-    " - {{output_md_trr}}: **Final trajectory** of the MD setup protocol.\n",
-    " - {{output_md_cpt}}: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.\n",
-    " - {{output_gppmd_tpr}}: **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.\n",
-    " - {{output_genion_top_zip}}: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).\n",
-    "\n",
-    "**Analysis** (MD setup check) output files generated:\n",
-    " - {{output_rms_first}}: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.\n",
-    " - {{output_rms_exp}}: **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.\n",
-    " - {{output_rgyr}}: **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.\n",
-    " "
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "***\n",
-    "<a id=\"questions\"></a>\n",
-    "\n",
-    "## Questions & Comments\n",
-    "\n",
-    "Questions, issues, suggestions and comments are really welcome!\n",
-    "\n",
-    "* GitHub issues:\n",
-    "    * [https://github.com/bioexcel/biobb](https://github.com/bioexcel/biobb)\n",
-    "\n",
-    "* BioExcel forum:\n",
-    "    * [https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library](https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library)\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.3"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb b/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
index 7d9facf..450b460 100644
--- a/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
+++ b/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
@@ -33,7 +33,7 @@
     "cd biobb_wf_md_setup\n",
     "conda env create -f conda_env/environment.yml\n",
     "conda activate biobb_wf_md_setup\n",
-    "jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb\n",
+    "jupyter-notebook biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb\n",
     "```\n",
     "\n",
     "***\n",