# Advanced simulation tutorials — input files

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
molecule, followed by Na and Cl.

### `experimental_rdf_oo_water_skinner2013.csv`
Experimental O–O radial distribution function of liquid water at 295.1 K, measured
by high-energy X-ray scattering.

Columns: `r_angstrom`, `g_oo`, `g_oo_error`

**Source:** Skinner, L.B. & Benmore, C.J. et al. *Benchmark oxygen-oxygen
pair-distribution function of ambient water from x-ray diffraction measurements with
a wide Q-range.* J. Chem. Phys. **138**, 074506 (2013).