Several molecular dynamics (MD) simulations of HIV-1 protease (HIV-1 PR)-substrate complex were performed. The initial structure of the enzyme-substrate (ES) complex was constructed based on the X-ray crystallographic structure of the HIV-1 PR-inhibitor (JG-365) complex. First, we investigate which of Asp25 and Asp25' at the catalytic site (two catalytic Asp residues) is protonated in the ES complex. These MD simulations have revealed that the protein hydrolysis mechanism is initiated from the ES complex in which Asp25' is protonated. This protein hydrolysis mechanism was already studied using quantum chemical calculations, which suggested that the specific conformation of the ES complex was essential for enzymatic activity. Next, we investigate the mechanism for the maintenance of specific conformation of the ES complex. The MD simulations suggest that two water molecules at the loop structures of the active site have a substantial role in maintaining the specific conformation for initiation of the enzyme reaction. This indicates that the enzymatic activity of HIV-1 PR cannot be induced by only the protease encoded by the RNA gene of HIV-1, but this also requires the incorporation of water molecules into the active site.