Open quantum system parameters for light harvesting complexes from molecular dynamics.

We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations-external or internal to the pigment molecules-enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up computationally more intensive calculations for a precise determination of spectral densities in the future. These are required to determine absorption spectra as well as transport properties of light harvesting complexes.