Molecular dynamics simulations of human immunodeficiency virus (HIV)-1 protease with a model substrate were used to test if there is a stable energy minimum for a proton that is equidistant from the four delta oxygen atoms of the two catalytic aspartic acids. The crystal structure of HIV-1 protease with a peptidic inhibitor was modified to model the peptide substrate Ser-Gln-Asn-Tyr-Pro-Ile-Val-Gln for the starting geometry. A proton was positioned between the two closet oxygen atoms of the two catalytic aspartic acids, and close to the carbonyl oxygen of the scissile bond in the substrate. All crystallographic water molecules were included. Two molecular dynamics simulations were run: 30 ps with united-atom potentials and 40 ps using the more accurate all-atom potentials. The molecular dynamics used a new algorithm that increased the speed and allowed the elimination of a cut-off for non-bonded interactions and the inclusion of an 8 A shell of water molecules in the calculations. The overall structure of the protease dimer, including the catalytic aspartic acids, was stable during the course of the molecular dynamics simulations. The substrate and a water molecule, that is an important component of the binding site, were stable during the simulation using all-atom potentials, but more mobile when united-atom potentials were used. A Poincare map representation showed that the positions of the proton and its coordinating oxygen atoms were stable for 93% of both simulations, although many of the buried and poorly accessible water molecules exchanged with solvent. The proton has a stable minimum energy position and maintains coordination with all four delta oxygen atoms of the two catalytic aspartic acids and the carbonyl oxygen of the scissile bond of the substrate. Therefore, a loosely bound hydrogen ion at this position will not be rapidly exchanged with solvent, and will rebond to either a catalytic aspartic acid or possibly the substrate. The implications for the reaction mechanism are discussed.