Keeping track of a hydrated proton in dynamics simulations is important and nontrivial. Here, we report two revised algorithms for the proton indicator, a pseudo-atom whose position approximates the location of an excess proton diffusing via the Grotthuss mechanism in aqueous solution. The new methods describe the delocalized proton as a structural defect. Encouragingly, in test simulations of a hydrated proton in bulk water, the new algorithms substantially outperform the original scheme by significantly reducing large displacements in the indicator positions upon donor switch, yielding smoother trajectories that effectively track the movement of the solvated proton.
Keywords: Adaptive QM/MM; Excess Proton; Grotthuss Mechanism; Molecular Dynamics; Solvation.