We present an analysis of different methods to calculate the classical electrostatic Hartree potential created by charge distributions. Our goal is to provide the reader with an estimation * To whom correspondence should be addressed † on the performance -in terms of both numerical complexity and accuracy-of popular Poisson solvers, and to give an intuitive idea on the way these solvers operate. Highly parallelisable routines have been implemented in the first-principle simulation code OCTOPUS to be used in our tests, so that reliable conclusions about the capability of methods to tackle large systems in cluster computing can be obtained from our work.

The complex photophysical properties of fluorescent proteins give rise to a wide field of applications as markers in molecular biology. Understanding these properties is essential for rational genetic engineering of new fluorescent proteins. Here, theoretical models are required to support the interpretation of structural and spectroscopic experimental data. This requires the accurate and reliable prediction of excited-state features of the chromophore and its interactions with the protein matrix. Here, we compare calculations of absorption and emission energies of semi-empirical (OM2/MRCI, ZINDO/S, and TD-DFTB) and ab initio (SORCI, CC2, and TDDFT) approaches for the HBDI chromophore in vacuo and wild-type green fluorescent protein (GFP) using QM/MM models. We discuss the influence of electrostatic fields, the chromophore geometry, the size of the QM region, and methodological aspects, in particular charge-transfer states in TDDFT and the applicability of real-space TDDFT codes. We revisit previous opposing theoretical studies and benchmark gas-phase measurements.Proton transfer wire of wild-type green fluorescent protein (wt-GFP).