From 44650ed9b877634bfe8261ebb902c3ee0b18ae62 Mon Sep 17 00:00:00 2001
From: Simon Gravelle <simon.gravelle@live.fr>
Date: Sat, 6 Jul 2024 14:49:00 +0200
Subject: [PATCH] adde dexercice

---
 docs/sphinx/source/journal-article.bib        | 11 +++++++
 .../source/tutorials/level1/bulk-solution.rst | 29 ++++++++++---------
 2 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/docs/sphinx/source/journal-article.bib b/docs/sphinx/source/journal-article.bib
index 7770db8..14b30db 100644
--- a/docs/sphinx/source/journal-article.bib
+++ b/docs/sphinx/source/journal-article.bib
@@ -193,6 +193,17 @@ @article{wong2016good
   publisher={Elsevier}
 }
 
+@article{sedlmeier2011spatial,
+  title={Spatial correlations of density and structural fluctuations in liquid water: A comparative simulation study},
+  author={Sedlmeier, Felix and Horinek, Dominik and Netz, Roland R},
+  journal={Journal of the American Chemical Society},
+  volume={133},
+  number={5},
+  pages={1391--1398},
+  year={2011},
+  publisher={ACS Publications}
+}
+
 @article{wang2020lennard,
   title={The Lennard-Jones potential: when (not) to use it},
   author={Wang, Xipeng and Ram{\'\i}rez-Hinestrosa, Sim{\'o}n and Dobnikar, Jure and Frenkel, Daan},
diff --git a/docs/sphinx/source/tutorials/level1/bulk-solution.rst b/docs/sphinx/source/tutorials/level1/bulk-solution.rst
index 128c43e..a1b3cfc 100644
--- a/docs/sphinx/source/tutorials/level1/bulk-solution.rst
+++ b/docs/sphinx/source/tutorials/level1/bulk-solution.rst
@@ -539,8 +539,8 @@ Energy minimization
 
 ..  container:: justify
 
-    The system is now in a favorable state and the molecular dynamics simulation
-    can be started.
+    Thank to the energy minimization, the system is now in a favorable state
+    and the molecular dynamics simulation can be started safely.
 
 Minimalist NVT input file
 =========================
@@ -1045,7 +1045,7 @@ Radial distribution function
 
     The radial distribution functions highlight the typical distance between
     the different species of the fluid. For instance, it can be seen that
-    there is a hydration layer of water around sodium ions at a typical
+    there is a strong hydration layer of water around sodium ions at a typical
     distance of :math:`2.4 ~ \text{Å}` from the center of the sodium ion.
 
 Mean square displacement
@@ -1112,17 +1112,20 @@ Mean square displacement
 
 .. include:: ../../non-tutorials/accessfile.rst
 
-..
-    Going further with exercises
-    ============================
 
-    Cage effect
-    -----------
+Going further with exercises
+============================
+
+..  container:: justify
 
-    ..  container:: justify
+    The solutions can be found in the GitHub repository of GROMACS tutorials.
 
-        The *cage effect* describes the dynamical confinement of a molecule
-        or an atom by its neighors. Modify *production.mdp* and probe the *cage effect*
-        for the sodium ions. Probe also the short-time ballistic regime.
+Calculate the structure factor
+------------------------------
+
+..  container:: justify
 
-        Cannot be done right now, because gmx msd does not like dt < 1 ps
\ No newline at end of file
+    Use the *gmx saxs* command and extract its structure factor, or :math:`S(q)`.
+    The structure factor is a fundamental quantity that it commonly measured
+    experimentally through Small Angle X-ray Scattering (SAXS) or Small-Angle
+    Neutron Scattering (SANS) :cite:`hansen2013theory, sedlmeier2011spatial`.
\ No newline at end of file