started restructuring tutorial 1

Author: simongravelle

docs/index.html

@@ -33,7 +33,7 @@ <h2>
                             <span class="image">
                                 <img src="avatars/level1/bulk-solution/bulk-solution-gromacs.png" alt="gromacs tutorial logo" />
                             </span>
-                            <a href="sphinx/build/html/tutorials/level1/bulk-solution.html">
+                            <a href="sphinx/build/html/tutorials/tutorial1/bulk-solution.html">
                                 <div class="content">
                                     <p align="left">
                                         Performing a <b>simple molecular dynamics</b>

docs/sphinx/source/index.rst

@@ -10,21 +10,11 @@ GROMACS tutorials
 
 .. toctree::
     :maxdepth: 2
-    :caption: Level 1
+    :caption: Tutorials
 
-    tutorials/level1/bulk-solution.rst
+    tutorials/tutorial1/bulk-solution.rst
     tutorials/level1/protein-in-electrolyte.rst
-
-.. toctree::
-    :maxdepth: 2
-    :caption: Level 2
-
     tutorials/level2/stretching-a-polymer.rst
-
-.. toctree::
-    :maxdepth: 2
-    :caption: Level 3
-
     tutorials/level3/solvation-energy.rst
     tutorials/level3/adsorption-ethanol.rst
 

docs/sphinx/source/journal-article.bib

@@ -278,6 +278,17 @@ @inproceedings{gowers2016mdanalysis
   organization={SciPy Austin, TX}
 }
 
+@article{van2005gromacs,
+  title={GROMACS: fast, flexible, and free},
+  author={Van Der Spoel, David and Lindahl, Erik and Hess, Berk and Groenhof, Gerrit and Mark, Alan E and Berendsen, Herman JC},
+  journal={Journal of computational chemistry},
+  volume={26},
+  number={16},
+  pages={1701--1718},
+  year={2005},
+  publisher={Wiley Online Library}
+}
+
 @article{michaud2011mdanalysis,
   title={{{MDAnalysis}}: a toolkit for the analysis of molecular dynamics simulations},
   author={Michaud-Agrawal, Naveen and Denning, Elizabeth J and Woolf, Thomas B and Beckstein, Oliver},

…ource/tutorials/level1/bulk-solution.rst …ce/tutorials/tutorial1/bulk-solution.rstdocs/sphinx/source/tutorials/level1/bulk-solution.rst renamed to docs/sphinx/source/tutorials/tutorial1/bulk-solution.rst docs/sphinx/source/tutorials/level1/bulk-solution.rst renamed to docs/sphinx/source/tutorials/tutorial1/bulk-solution.rst

@@ -19,16 +19,18 @@ Bulk salt solution
     :height: 250
     :align: right
 
-The objective of this tutorial is to use the
-open-source code GROMACS to perform a simple molecular
-dynamics simulation. The system is a bulk solution of water mixed
-with sodium (Na\ :sup:`+`) and sulfate
-(SO\ :sub:`4`\ :sup:`2-`) ions. 
-
-This tutorial illustrates several major ingredients of molecular
-dynamics simulations, such as energy minimization,
-thermostating, NVT and NPT equilibration, and
-trajectory visualization.
+The objective of this tutorial is to use the open-source code GROMACS
+:cite:`van2005gromacs` to perform a molecular dynamics simulation. The
+system consists of a bulk solution of water mixed with sodium
+(Na\ :sup:`+`) and sulfate (SO\ :sub:`4`\ :sup:`2-`) ions.
+
+This tutorial demonstrates how to set up a simulation box, solvate it
+with water, and add ions. It also introduces key components of molecular
+dynamics simulations, including energy minimization, thermostating, and
+*NVT* and *NpT* equilibrations. The resulting trajectory is analyzed
+using GROMACS utilities to extract properties such as the radial distribution
+function (RDF) and mean squared displacement (MSD). Trajectories are
+visualized using VMD :cite:`humphrey1996vmd`.
 
 .. include:: ../../non-tutorials/needhelp.rst
 .. include:: ../../non-tutorials/GROMACS2024.2.rst