Merge pull request #25 from gromacstutorials/small-grammar-improvement

Small grammar improvement

Author: simongravelle

docs/index.html

@@ -47,7 +47,7 @@ <h2>
                             <span class="image">
                                 <img src="avatars/level1/protein-in-electrolyte/protein-in-electrolyte.png" alt="gromacs tutorial logo" />
                             </span>
-                            <a href="sphinx/build/html/tutorials/level1/protein-in-electrolyte.html">
+                            <a href="sphinx/build/html/tutorials/tutorial2/protein-in-electrolyte.html">
                                 <div class="content">
                                     <p align="left">
                                         Simulating a <b>protein</b> in an electrolyte
@@ -59,7 +59,7 @@ <h2>
                             <span class="image">
                                 <img src="avatars/level2/stretching-a-polymer/stretching-polymer-gromacs.png" alt="gromacs tutorial logo" />
                             </span>
-                            <a href="sphinx/build/html/tutorials/level2/stretching-a-polymer.html">
+                            <a href="sphinx/build/html/tutorials/tutorial3/stretching-a-polymer.html">
                                 <div class="content">
                                     <p align="left">
                                         Stretching a <b>polymer</b> in water

docs/sphinx/source/index.rst

@@ -13,8 +13,8 @@ GROMACS tutorials
     :caption: Tutorials
 
     tutorials/tutorial1/bulk-solution.rst
-    tutorials/level1/protein-in-electrolyte.rst
-    tutorials/level2/stretching-a-polymer.rst
+    tutorials/tutorial2/protein-in-electrolyte.rst
+    tutorials/tutorial3/stretching-a-polymer.rst
     tutorials/level3/solvation-energy.rst
     tutorials/level3/adsorption-ethanol.rst
 

docs/sphinx/source/non-tutorials/links.rst

@@ -44,4 +44,100 @@
 
 .. |patreon| raw:: html
 
-    <a href="https://www.patreon.com/molecularsimulations" target="_blank">patreon</a>
+    <a href="https://www.patreon.com/molecularsimulations" target="_blank">patreon</a>
+
+.. |Protein-Data-Bank| raw:: html
+
+   <a href="https://www.rcsb.org/structure/1CTA" target="_blank">Protein Data Bank</a>
+
+.. |1cta-pdb| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level1/protein-in-electrolyte/1cta.pdb" target="_blank">1cta.pdb</a>
+
+.. |trjconv| raw:: html
+
+   <a href="https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html" target="_blank">trjconv</a>
+
+.. |empty.gro| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/empty.gro" target="_blank">empty.gro</a>
+
+.. |Gromos87| raw:: html
+
+    <a href="https://manual.gromacs.org/archive/5.0.4/online/gro.html" target="_blank">Gromos87</a>
+
+.. |so4.gro| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/so4.gro" target="_blank">so4.gro</a>
+
+.. |insert-molecules| raw:: html
+
+    <a href="https://manual.gromacs.org/2025.1/onlinehelp/gmx-insert-molecules.html" target="_blank">insert-molecules</a>
+
+.. |na.gro| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/na.gro" target="_blank">na.gro</a>
+
+.. |h2o.gro| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/h2o.gro" target="_blank">h2o.gro</a>
+
+.. |conf_gro_tutorial1| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/conf.gro" target="_blank">conf.gro</a>
+
+.. |topol-SO4.top| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/topol.top" target="_blank">topol.top</a>
+
+.. |forcefield.itp| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/forcefield.itp" target="_blank">forcefield.itp</a>
+
+.. |h2o.itp| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/h2o.itp" target="_blank">h2o.itp</a>
+
+.. |na.itp| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/na.itp" target="_blank">na.itp</a>
+
+.. |so4.itp| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/so4.itp" target="_blank">so4.itp</a>
+
+.. |steepest-descent| raw:: html
+
+    <a href="https://manual.gromacs.org/current/reference-manual/algorithms/energy-minimization.html" target="_blank">steepest-descent</a>
+
+.. |grace| raw:: html
+
+    <a href="https://plasma-gate.weizmann.ac.il/Grace/" target="_blank">Grace</a>
+
+.. |leap-frog| raw:: html
+
+   <a href="https://manual.gromacs.org/nightly/reference-manual/algorithms/molecular-dynamics.html#update" target="_blank">leap-frog</a>
+
+.. |Liese2017| raw:: html
+
+   <a href="https://doi.org/10.1021/acsnano.6b07071" target="_blank">Liese</a>
+
+.. |peg-gro| raw:: html
+
+   <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/peg.gro" target="_blank">peg.gro</a> 
+
+.. |video_peg_youtube| raw:: html
+
+   <a href="https://www.youtube.com/watch?v=8ldIHP175TI&t=9s" target="_blank">video</a>
+
+.. |download_charmm35r.itp| raw:: html
+
+   <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/ff/charmm35r.itp" target="_blank">charmm35r.itp</a>
+   
+.. |download_peg.itp| raw:: html
+
+   <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/ff/peg.itp" target="_blank">peg.itp</a>
+
+.. |download_tip3p.itp| raw:: html
+
+    <a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/ff/tip3p.itp" target="_blank">tip3p.itp</a>