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).