Molecular dynamics simulation of complex reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) soft- ware package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time- scales is a challenging task. Ab initio methods are unable to currently access these timescales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Mul- tiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer timescale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations towards the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.