Update advanced_simulation/README.md

advanced_simulation/README.md

@@ -1,9 +1,25 @@
-# Advanced simulation tutorial — input files
+# Advanced simulation tutorials — input files
 
-This directory contains the input files used by `advanced_simulation_tutorial.ipynb`.
+This directory contains the input files used by 
+  - `advanced_simulation_tutorial.ipynb`
+  - `metadynamics_tutorial.ipynb`
+  - `fep_tutorial.ipynb`
 
 ## Files
 
+### `methane_minimized.pdb`
+Pre-minimized rhombic dodecahedron box containing one methane molecule, and 234 
+water molecules, with 11A padding between the methane molecule and the outer edge 
+(707 atoms total). The first 5 atoms are the methane molecule, with the following
+atoms ordered as consecutive OHH triplets for each water molecule. Used in the 
+FEP tutorial, where we predict the hydration free energy of methane.
+
+### `methane_molecule_indices.npy`
+Pre-computed "molecules indices" array for the `methane_minimized` system, 
+containing a per-atom molecule assignment required for running an NPT simulation
+using a Monte Carlo barostat. Used in the FEP tutorial, where we predict the 
+hydration free energy of methane.
+
 ### `nacl_equil.xyz`
 Pre-equilibrated cubic box of 106 water molecules and one NaCl ion pair (320 atoms,
 box length ≈ 14.7 Å). Atoms are ordered as consecutive OHH triplets for each water