Faunus Notebooks

This repository contains Jupyter Notebooks for running Faunus, a framework for Metropolis Monte Carlo simulations.

Description of the notebooks:

Metropolis Monte Carlo

• pH titration of a protein - explicit, grand canonical salt (incl. all-atom to amino acid coarse graining)
• A salt solution in contact with a surface with titrating surface sites
• Melted salt with off-center charges (incl. parallel tempering of the dielectric constant)
• PMF of rigid fibril in contact with a charged surface (incl. sbatch submit script, Debye-Hückel electrostatics)
• Free energy between two rigid bodies in explicit salt and constant pH
• Uniformly distribute charges on a sphere using hyperspherical geometry

Statistical mechanical theory

• Equation of state using generalized van der Waals theory (interactive plot)
• Electric multipole interactions: MC, Keesom etc.