GROMACS version: 2018
GROMACS modification: Yes/No
I want to know whether we can change the pH (pH other than body pH) of a solution containing enzyme we are simulating and how can we do that? Is there any option for that in md parameter file?
You can either set a fixed protonation state with the constituent molecules ionized as they would be at a given pH according to their pKa values, or perform constant-pH simulations, which is a special technique. You do not typically set a value of pH in a simulation system in a standard setup because there are no dissociable protons and the concentration of H3O+ would not be anywhere near realistic.