Figure : Schematic of the internal structure of phbuilder, as well as the movement of various input and output files and external GROMACS programs and scripts utilized. phbuilder consists of three tools: gentopol, neutralize and genparams. gentopol prepares the structure and topology files, neutralize ensures the appropriate number of ions and buffer particles for a net-neutral system, and genparams generates the .mdp and .ndx parameter files required for running constant pH MD in GROMACS.