CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations.

Abstract

Molecular mechanical (MM) force fields are constructed based on the empirical potentials, describing intramolecular and intermolecular potentials. Molecular dynamics (MD) simulation utilizing MM force fields is a robust tool to investigate large biomolecular systems, but the changes in electronic structures during a chemical process are overlooked in classical mechanics. Quantum mechanical (QM) treatments are needed for such changes including bond forming/breaking and charge transfers, but a high computational cost limits its usages with up to hundreds of atoms or less. A hybrid QM/MM approach, where the reactive part of the system is treated with QM and the remainder by cheap MM potentials, can effectively capture the reaction without significantly increasing the computational cost. For the different nature of the QM versus MM theories, however, the setup of biomolecular QM/MM simulation is known to be time consuming even to QM/MM experts. We present CHARMM-GUI QM/MM Interfacer that prepares QM/MM simulations with a user-selected QM region and various QM theories in multiple simulation packages. A non-trivial and error-prone QM/MM simulation setup involving link-atom insertion and charge distribution can be seamlessly prepared in QM/MM Interfacer. A few representative systems are simulated to delineate the robustness of QM/MM Interfacer. We hope both QM/MM beginners and experts to find the module's quick and accurate QM/MM simulation setup useful for their important applications.