| # 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). |
| |
