Molecular dynamics (MD) simulations of biomolecular systems are nowadays widely applied to study a broad range of research questions, from protein folding 1 to designing drugs. While parameters such as temperature and pressure are routinely taken into account in MD simulations, pH, a critical parameter influencing the structure, dynamics, and function of many biomolecules, 3 cannot be controlled in standard MD. To overcome this limitation and capture the effects of pH, constant pH simulation methods have been developed. We have recently presented an efficient implementation of continuous constant pH for the GROMACS MD package, based on the λ-dynamics approach first introduced by Brooks and co-workers in 1996. Similar implementations are also available in other popular MD software packages such as CHARMM and AMBER. While progress has been made in refining the methodological aspects of constant pH MD, the setup of such simulations remains complicated. Setup requires several steps, including preparation of the initial structure, and modifying topology and parameter files. Structure preparation requires adding dummy hydrogens to all titratable groups in the system, topology modification requires assigning charges for all protonation states of titratable groups, and modification of parameter files includes the addition of parameters specific for constant pH MD simulations. Although these are general steps for constant pH MD, implementation details of such setup steps can differ significantly between MD engines and often require time-consuming and error-prone manual modifications. Setting up constant pH MD also requires a deep understanding of the system's chemistry and force field formatting which is also specific for a particular MD engine.