Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials
Y. Tao, T. J. Giese, Ş. Ekesan, J. Zeng, B. Aradi, B. Hourahine, H. M. Aktulga, A. W. Götz, K. M. Merz, Jr., and D. M. York J. Chem. Phys. 160 , 224104 (2024) We report the development and testing of new [...] semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated [...] demonstrated on proton transfer reactions in guanine- thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing