The cleavage mechanism of HIV-1 protease is investigated with molecular dynamics simulation of substrate-, inhibitor-, and gem-diol intermediate-bound protease. Initial structures are based on X-ray crystallographic coordinates for the protease bound to the inhibitor JG-365.(1,2) The conformation space explored by atoms near the active site on the 100 ps time scale at 300 K is analyzed for structures likely to initiate reaction. Conformations suitable for reaction initiation are generated for both general acid-general base and direct nucleophilic attack mechanisms. The simulations suggest that (1) both types of mechanism are plausible; (2) the catalytic Asp of monomer B is protonated when reaction begins; (3) if the mechanism is general acid-general base, the catalytic Asp of monomer A is protonated when the second reaction step is initiated; (4) the carbonyl oxygen is more likely than the scissile nitrogen to be protonated in the early stages of reaction; (5) water 301(1) stabilizes productive conformations of reactants and intermediates, but it does not participate directly in reaction; and (6) a lytic water, if present, has very little mobility.