Software

Hybrid and hierarchical approach to study molecular systems in complex environments. We combine three different approaches and tools in computational chemistry: quantum dynamics (Quantics/MCTDH), quantum mechanics (Q-Chem), and molecular mechanics (Gromacs). To ensure a seamless interaction between software packages, we previously developed PySurf (framework for database accelerated direct dynamics, hosting a surface point provider as its core that communicates with a neural network plugin), INAQS (generic QM/MM interface for non-adiabatic dynamics) and Q-Force (automated tool to generate quantum mechanically derived force fields).

PySurf: M. F. S. J. Menger, J. Ehrmaier, S. Faraji* (2020), PySurf: Databased Accelerated Surface Hopping", J. Chem. Theory Comput., 16(12), 7681. https://doi.org/10.1021/acs.jctc.0c00825 

INAQS: V. Cofer-Shabica*, M. F. S. J. Menger, Q. Oui, Y. Shao, J. E. Subotnik, S. Faraji* (2022), "INAQS: a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations", J. Chem. Theory Comput., 18, 8, 4601. https://doi.org/10.1021/acs.jctc.2c00204 

Q-Force: S. Sami*, M. F. S. J. Menger, S. Faraji, R. Broer, R. Havenith, (2021), "Q-Force: Quantum Mechanically Augmented Molecular Force Fields", J. Chem. Theory Comput., 17(8), 4946. https://doi.org/10.1021/acs.jctc.1c00195