Modelling a given pH value explicitly, i.e. via introducing a certain number of H3O+ ions is normally difficult because, unless you go to very extreme pH values, the H3O+ concentration is so low that you'd have to use a huge number of water molecules. That also requires that you'd need to use DFT or at least a very good reactive force field, to correctly model proton transfer.
Another more implicit approach is, if you know what effect the pH has on your system (e.g. if you have acidic groups) , to manually fix the protonation state of these groups according to the given pH, e.g. if you have an acidic group and you want to simulate neutral pH, the acidic group would most likely be present in the deprotonated state.
A good thing to start with could be to try and find out what the effect of pH is on the components of your system, for example if water molecules might dissociate at the edges of your graphene flake, leading to adsorbed OH groups, whose behavior might then be pH dependent.
