Figure 6. Averaged radial distribution functions $g\left(r\right)$ between His146 and water for the different box sizes and for simulation windows before, during and after the structural transitions (see Figure 1).

Analysis for (A) the C-terminal (CT) of His146 and Water H (Hw) and (B) for C of His146 and water O (Ow). For the largest (150 Å) box no appreciable change in $g\left(r\right)$ is found. The two peaks at 2.7 and 4.1 Å in (A) and the two peaks at 5 and 7.5 Å in (B) are due to a water network as indicated in the sketches. The sketches in A and B represent different views of the same snapshot taken from the MD simulation of the 150 Å box at $t=960$ ns and is used here as reference to describe the water network because this box represented a stable $g\left(r\right)$. Sketches in (A) emphasise the water network at the C-terminal of His146, and sketches in (B) emphasise the water network at the C${}_{\gamma }$ of His146. Waters W0, W1 and W2 are key structural waters (used as anchor) in the stability of the T state (they are framed with a black line). This network is stable for simulations in the largest box but unstable in the other boxes. His143 is singly protonated (${\displaystyle \mathrm{N}ϵ}$) and His146 is doubly protonated (N$\delta$ and N$ϵ$).