Goran Giudetti

Project Details

This study investigates the necessary transparency in reporting computational protocols for achieving practical reproducibility in quantum mechanics/molecular mechanics (QM/MM) simulations. Utilizing the reaction between the main protease of SARS-CoV-2 and the covalent inhibitor carmofur as a case study for chemical reactions in biomolecules, QM/MM calculations were conducted to determine structures, energies of reactants, products, and transition states/intermediates. This analysis employed analogous QM/MM models in two software packages, NWChem and Q-Chem, with the primary benchmarking goal of reproducing key energetics computed by both packages. The results highlight the challenge of achieving quantitative agreement within specified numerical thresholds. The study underscores the necessity of reporting even minor details of QM/MM simulations for result reproducibility and offers recommendations for practical guidelines in reporting biosimulation outcomes.