Correction to "Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides".

2020

GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation

2020

Atomistic simulations of large biomolecular systems with chemical variability such as constant pH dynamic protonation offer multiple challenges in high performance computing. One of them is the correct treatment of the involved electrostatics in an efficient and highly scalable way. Here we review and assess two of the main building blocks that will permit such simulations: (1) An electrostatics library based on the Fast Multipole Method (FMM) that treats local alternative charge distributions with minimal overhead, and (2) A $λ$-dynamics module working in tandem with the FMM that enables various types of chemical transitions during the simulation. Our $λ$-dynamics and FMM implementations d…