Large-scale QM/MM calculations of electronic excitations in yellow protein: Toward petascale level of protein calculations

Large-scale combined quantum mechanical - molecular mechanical (QM/MM) calculations of an active-site of the photoactive yellow protein have been performed. The calculations are based on a 10 ns molecular dynamics simulation of the protein, and a 10 ns molecular dynamics of the protein chromophor in water solution, using AMBER force fields. For each of these simulations, 1,000 randomly chosen configurations were selected and individual combined QM/MM calculations for each configuration were performed. The QM/MM calculations included geometry optimization of the protein chromophor calculated at the AMBER/B3LYP/6-31+G* level of theory, and electronic-excitation calculations performed at the AMBER/TDDFT/B3LYP/aug-cc-pVTZ level of theory. Final results are reported as averaged data based on an ensemble of 1,000 structures obtained from the molecular dynamics simulations. The results of the calculations are compared with experimental data of electronic excitations of the protein photoreceptor in the protein, in water solution and in the gas phase.