Flow diagram for preparation of protein:membrane model for QM/MM calculations.

Blue stages correspond to preparation steps whereas pink stages involve molecular dynamics (MD) simulations and QM/MM calculations. In the initial step (yellow) the structure of the protein of interest is downloaded from the PDB. The following steps describe the unbiased coarse grained (CG) set up of a protein in the presence of a chosen lipid composition. Following these preparatory stages CGMD simulations are run to allow the bilayer to self-assemble in an unbiased manner around the protein. This CGMD protein-membrane simulation box may be converted to atomistic resolution and atomistic MD simulations performed to look at conformational changes. The outcome of these simulations may then be used as the basis of QM/MM calculations or other calculations of interest.