Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

This article recapitulates the state of the art regarding simulations of ionization equilibria of
weak polyelectrolyte solutions and gels. We start out by reviewing the essential …

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic
trajectories of complex systems. Systems are simulated in various ensembles, depending on …

Various approaches have been proposed to include the effect of pH in molecular dynamics
(MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co …

A molecular-scale understanding of the transition between hydration states in clay minerals
remains a challenging problem because of the very fast stepwise swelling process observed …

Protonation states of ionizable protein residues modulate many essential biological
processes. For correct modeling and understanding of these processes, it is crucial to …

Salts reduce the p K a of weak acids by a mechanism sensitive to ion identity and
concentration via charge screening of the deprotonated state. In this study, we utilize …

Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His,
making up≈ 25% of the residues. The protonation state of residues, cofactors, and ligands …

Alchemical free energy calculations using conventional molecular dynamics and
thermodynamic integration rely on simulations performed at fixed values of the coupling …

The pK a is the standard measure used to describe the aqueous proton affinity of a
compound, indicating the proton concentration (pH) at which two protonation states (eg A …