Add Enhanced sampling simulation cookbooks

.gitignore

@@ -141,3 +141,6 @@ cython_debug/
 build
 .ipynb_checkpoints
 openmm
+
+# MacOS specific files
+.DS_Store

cookbook.md

@@ -26,6 +26,10 @@ notebooks/cookbook/Changing Temperature and Pressure
 notebooks/cookbook/Saving Systems to XML Files
 notebooks/cookbook/Merging Molecules
 notebooks/cookbook/Adding Hydrogens to Nonstandard Molecules
+notebooks/cookbook/Enhanced sampling methods/Accelerated MD
+notebooks/cookbook/Enhanced sampling methods/Gaussian Accelerated MD
+notebooks/cookbook/Enhanced sampling methods/Metadynamics
+notebooks/cookbook/Enhanced sampling methods/Umbrella sampling MD
 :::
 
 ## Restraints, Constraints, and External Forces

index.md

@@ -15,6 +15,41 @@ These can also be run in Colab, but due to the longer compute time required (ten
 hidden: true
 maxdepth: 3
 ---
-cookbook.md
-tutorials.md
+notebooks/cookbook/Changing Temperature and Pressure
+notebooks/cookbook/Saving Systems to XML Files
+notebooks/cookbook/Merging Molecules
+notebooks/cookbook/Adding Hydrogens to Nonstandard Molecules
+:::
+
+## Restraints, Constraints, and External Forces
+
+:::{nbgallery}
+---
+glob: True
+caption: Restraints, Constraints, and External Forces
+---
+notebooks/cookbook/Applying a Constant External Force
+notebooks/cookbook/Constraining Atom Positions
+notebooks/cookbook/Restraining Atom Positions
+notebooks/cookbook/Restraining Dihedrals
+:::
+
+## Analysis and System Inspection
+
+:::{nbgallery}
+---
+glob: True
+caption: Analysis and System Inspection
+---
+notebooks/cookbook/Analyzing Energy Contributions
+notebooks/cookbook/Querying Charges and Other Parameters
+:::
+
+## Tutorials
+
+:::{nbgallery}
+---
+glob: True
+caption: Tutorials
+---
 :::