Open quantum system parameters from molecular dynamics

TL;DR

This paper combines molecular dynamics simulations and energy gap calculations to extract site energies and spectral densities of the FMO complex, analyzing methodological differences and their impact on results, with implications for future computational studies.

Contribution

It systematically compares different simulation methods to understand their effects on spectral density extraction, providing guidance for more accurate future calculations.

Findings

Different forcefields significantly affect site energies and spectral densities.

Averaged results align well with experimental data.

Vibrations internal and external to pigments influence the spectral quantities differently.

Abstract

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 more computationally 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.