Understanding and controlling chemical reactivity in biological systems require atomic-level insight into processes that are often inaccessible to experiments. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful framework for describing chemical reactions in complex environments, but their practical application remains limited by fragmented software ecosystems, restricted accessibility, and methodological approximations that can compromise accuracy and reproducibility. In particular, many existing QM/MM implementations rely on ad hoc couplings, proprietary software, or truncated treatments of long-range electrostatic interactions. Here, we present a robust and fully periodic QM/MM interface between the open-source molecular dynamics engine GROMACS and the electronic structure theory code CP2K. The implementation enables efficient and reproducible QM/MM molecular dynamics and enhanced sampling simulations with a consistent treatment of long-range electrostatics under periodic boundary conditions. By combining the strengths of two widely used community codes, this interface provides a general and scalable platform for studying chemical reactivity in biological systems and establishes a transparent reference implementation for QM/MM simulations.
D. Morozov, C. Blau, Ole Schütt et al.· Journal of Chemical Informat...· 0 citations
Experiments indicate that collective coupling of molecular ensembles to confined optical modes can modify excited-state dynamics and photochemical reactivity. To describe such cavity-induced effects at atomic resolution, semi-classical molecular dynamics approaches have been developed that treat nuclear motion classically while describing the collective light-matter interaction within the Tavis-Cummings framework of quantum electrodynamics. Here, we benchmark mixed quantum-classical approaches, Ehrenfest dynamics, and Fewest-Switches Surface Hopping (FSSH) for simulating nonadiabatic dynamics of electronically strongly coupled carbon monoxide molecules. Their predictions are compared against numerically exact quantum dynamics simulations performed with the multi-configuration time-dependent Hartree method, which treats both electronic and nuclear degrees of freedom quantum mechanically. We find that the semi-classical approaches reproduce the qualitative features of the full quantum dynamics. Quantitative agreement is best achieved with FSSH when a decoherence correction is included. These results demonstrate that mixed quantum-classical methods provide a computationally efficient and quantitatively reliable alternative to fully quantum simulations for investigating nonadiabatic photochemistry under collective electronic strong coupling in systems beyond the reach of exact quantum treatments.
Arun Kumar Kanakati, Oriol Vendrell, G. Groenhof· Journal of Chemical Physics· 0 citations
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