Figure 9.

Ion translocation in the KcsA K⁺ channel described by self-learning umbrella sampling. The 2D PMF is shown at different stage of the umbrella sampling calculations: starting with 9 windows (a), moving to 25 (b) and 28 windows (c). The final PMF shown in (d) was calculated from 63 windows. The reaction coordinates are the center-of-mass of ions K¹ and K² along the Z axis, $\mathit{CoM}(K_Z^1,K_Z^2)$, and the position of ion K ³ along the same axis, $K_Z^3$.