pH-Dependent Vibrational Dynamics Drives Excited-State Quenching in the Phycobiliprotein Complex PC645

The folder MD contains the mdp and structure files required for equilibration, the tpr and xtc trajectory files from a 1 μs classical MD simulation (with only 1000 frames retained), as well as, for each pigment molecule, the tpr and xtc trajectory files from a 1 ns QM/MM simulation (also reduced to 1000 frames), together with the QM/MM-optimized structures. The other folders contain the site energies (eV), spectral densities (cm⁻¹), and TrESP charges of the individually QM/MM-optimized pigment molecules.