To show that phbuilder may also be used to set up more complex systems, we next used it to set up a constant pH simulation for the pentameric ion channel GLIC, embedded in a POPC bilayer. Although membrane embedding cannot be performed with phbuilder, we successfully managed to take an embedded structure (generated from CHARMM-GUI) and use the tool to set up the constant pH input files from there. A subsequent 10 ns simulation proved the system was stable (Figure ).