Figure 6.

Average solvent accessible surface area of the fusion peptide in constant-pH MD simulations. The fusion peptide solvent accessible surface area (SASA) was computed with the GROMACS g_sas tool, which implements the algorithm described by Eisenhaber et al.⁵⁶ The average SASA value for each replicate at each pH value was calculated over the last 400 ns of simulation for the simulation set H (left side) and V (right side). Each point corresponds to an independent replicate simulation performed in a given pH value (the color codes used are describe in Fig. 4) and the black line passes through the average value computed over all the replicates simulated at a given pH value.