Next, the names of atoms that have different charges in different protonation states of the residue are given. The atomic charges of two protonated states should be provided as qqA and qqB 1 entries. The order of charges should correspond to the order of atom names. Then, the pK a value of the titratable group in water, as well as the coefficients of the polynomial fit of the correction potential V MM are provided. For more details on V MM , please check the GROMACS constant pH publication and repository. For titratable groups described with the multi-site representation (such as histidine with three protonation states), details of each protonation state should be listed: The multi-site representation allows simulation of chemically coupled titratable sites. In general, if a group can be found in N different protonation states, the multi-site representation will include N + 1 states: one artificial common state, and N physical states of the group. The charges for the common state (which are usually zeros) should be provided as qqA. For each physical state i the corresponding pK a values, charges, and polynomial coefficients of correction potential should be provided as pKa i, qqB i, and dvdl i, respectively.