improved tutorial

Author: simongravelle

docs/sphinx/source/journal-article.bib

@@ -5,6 +5,17 @@ @book{barrat2003basic
   publisher={Cambridge University Press}
 }
 
+@article{shaw1992determination,
+  title={Determination of the solution structure of a synthetic two-site calcium-binding homodimeric protein domain by NMR spectroscopy},
+  author={Shaw, Gary S and Hodges, Robert S and Sykes, Brian D},
+  journal={Biochemistry},
+  volume={31},
+  number={40},
+  pages={9572--9580},
+  year={1992},
+  publisher={ACS Publications}
+}
+
 @article{bank1971protein,
   title={Protein data bank},
   author={Bank, Protein Data},

docs/sphinx/source/tutorials/level1/protein-in-electrolyte.rst

@@ -22,8 +22,10 @@ Convert the pdb file
 
 .. container:: justify
 
-    Download the *.pdb* file from the |ProteinDataBank|, or simply
-    click |1cta.pdb|.
+    Download the *.pdb* file from the |ProteinDataBank|,
+    or simply click |1cta.pdb|. The protein is a calcium-binding peptide from site III
+    of chicken troponin-C that has been determined using 1H-NMR
+    spectroscopy :cite:`shaw1992determination`.
 
 .. |ProteinDataBank| raw:: html
 
@@ -33,4 +35,43 @@ Convert the pdb file
 
     <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level1/protein-in-electrolyte/1cta.pdb" target="_blank">here</a>
 
+.. container:: justify
+
+    We first need to create the *.gro* file, i.e. a GROMACS structure file,
+    from the *.pdb* file. This can be done using *gmx trjconv*:
+
+.. container:: bash
+
+    gmx trjconv -f 1cta.pdb -s 1cta.pdb -o 1cta.gro -center -box 5 5 5
+
+.. container:: justify
+
+    Choose the group *System* for the centering, and the group *System* as well 
+    for the output. A file named *1cta.gro* is created. The generated *.gro*
+    file contains 666 atoms, each atom corresponding to one line:
+
+.. container:: bash
+
+    TROPONIN C SITE III - SITE III HOMODIMER
+    666
+        0ACE      C    1   2.662   4.131   2.701
+        0ACE      O    2   2.714   4.036   2.646
+        0ACE    CH3    3   2.651   4.147   2.853
+    (...)
+   35NH2    HN2  664   2.417   3.671   3.192
+   69CA      CA  665   3.016   2.279   1.785
+   70CA      CA  666   1.859   2.046   1.838
+   5.00000   5.00000   5.00000
+
+.. container:: justify
+
+    The last line is the box dimensions in nanometer, which was requested 
+    in the *gmx trjconv* command by the *-box 5 5 5* option. All the options
+    of *trjconv* can be found in the corresponding page of the GROMACS
+    |trjconv-documentation|.
+
+.. |trjconv-documentation| raw:: html
+
+    <a href="https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html" target="_blank">documentation</a>
+
 .. include:: ../../non-tutorials/accessfile.rst