Monte Carlo methods to simulate acid/base equilibria in ESPResSo
When chemical reactions are present in macromolecular systems, they can significantly impact the physical properties of these systems. For example, weak polyelectrolytes and biomacromolecules can modulate their charge in response to their microenvironment through the acid/base equilibrium, a phenomenon known as charge regulation. To simulate this kind of systems, the configuration space and the reaction degrees of freedom need to be simultaneously sampled because they are highly coupled. Nowadays, Monte Carlo (MC) simulations and coarse-grained models have become a popular approach to study these systems because they permit efficient sampling of their equilibrium properties. In this lecture, we will showcase the reactive Monte Carlo methods available in ESPResSo and we will discuss their applicability for different case scenarios. Furthermore, we will present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software with tools to aid the setup of these MC simulations for custom coarse-grained models and pre-defined models of peptides and globular proteins in ESPResSo.