The mechanism of the first steps of the reaction catalyzed by HIV1~protease (HIV1~PR) was studied through molecular dynamics simulations (MD/AVB). The potential energy surface in the active site was generated using the Approximate Valence Bond (AVB) method. The AVB method was parameterized based on density functional (DFT) calculations. The surrounding protein and explicit water environment was modeled with conventional, classical force field. The calculations were performed based on HIV1 PR complexed with the MVT-101 inhibitor that was modified to a model substrate. The protonation state of the catalytic aspartates was determined theoretically. Possible reaction mechanisms involving the lytic water molecule are accounted for in this study. The modeled steps include the dissociation of the lytic water molecule and proton transfer onto Asp-125, the nucleophilic attack followed by a proton transfer onto peptide nitrogen. The simulations show that in the active site most preferable energetically are structures consisting of ionized or polarized molecular fragments that are not accounted for in conventional MD. The mobility of the lytic water molecule, the dynamics of the hydrogen bond network, and the conformation of the aspartates in the active centre were analyzed.