Atomistic Simulations of Ion Channels - Computational Neuroscience: A Comprehensive Approach - page 38

Figure 2.3
Different schemes to separate interesting from less interesting regions in simula-
tions. A. The partitioning of a system for BD calculations proposed by Im and Roux.
Reproduced with permission from [63]. B. The partitioning of the system used by
Burykin et al. The area within the black square is explicitly represented in the sim-
ulation. Reproduced with permission from [23]. Simulation methods used in both
studies are different, but have in common that the interior of the protein is treated in
most detail, whereas remote regions of the solvent and membrane are treated in very
little detail.