I am working on the simulations of lipids and cholesterol (DPPC+DPPG+CHOL) forming bi-layers in different pHs (e.g. pH=5.5 and 6.5 solutions).
May I please know if the protonation needs to be considered in my simulation using MARTINI FF? If that is the case, could you share some information/steps how I can protonate them using MARTINI FF?
Any help and information will be really appreciated!