1BRS ) and (3) the proton-gated ion channel GLIC (PDB ID: 6ZGD 47 ). The structures for these proteins are shown in Figure . For cardiotoxin V, we used phbuilder to set up the system starting from a .pdb file from the Protein Data Bank 41 as well as from the prepared simulation system. For the barnase-barstar complex, phbuilder was used to demonstrate the preparation of a system with multiple chains from a .pdb file. We also used the tool to set up constant pH MD for an existing GLIC membrane system.