Nile red or 9-(diethylamino)-5H -benzo[a]phenoxazin-5-one (shown in Figure ) was used for the investigations of heterogeneous environments. NR is a lipophilic neutral fluorescent molecule used as a membrane dye due to its strong solvatochromic properties. For the same reason, it is a good candidate for computational studies of environmental effects. Here we use two biomolecular environments: the β-lactoglobulin (BLG) protein (Figure ) and a lipid bilayer consisting 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids (Figure ). Both systems are solvated in water and include ions. The simulation box dimensions and the number of atoms are provided in Table2. The structures of NR embedded in the BLG protein were provided by Hartmann et al. The structures were extracted from 75 independent 1.5 ps electrostatic embedding QM/MM MD trajectories that were started from equidistant points of a classical MD trajectory. The QM subsystem consisted of the NR molecule, which was treated at M06L 57 /def2-SVP 58 level of theory, and the remainder constituted the MM subsystem, which was modeled using the ff14SB 59 force field. Two configurations were extracted from each trajectory resulting in 150 configurations in total.