The contribution of water molecules in molecu-lar dynamics simulation (MDS) is unquestiona-bly high, particularly for enzymatic interaction which occurred in the cytoplasmic environment. The addition of water molecules to the system will surely influence different direct interaction between active site residues and substrate. We try to theoretically investigate to what extent the pathogenicity characterization will varies in dif-ferent neuraminidase-sialic acid complex sys-tems. The heating dynamics simulations were produced with and without TIP3P water mole-cules. The periodic boundary system was made for explicitly added TIP3P water molecules and generalized born molecular volume (GBMV) en-ergy contribution was added for implicit solvent system. Both complexes, neuraminidase-sialic acid of A/Tokyo/3/67 and A/Pennsylvania/10218/ 84, which have a different pathogenicity levels were minimized and simulated. The result shows more residues produced hydrogen bonds with substrate when water molecules were not added to the system. The binding free energies also show differences. Overall, even the values of energy is different, but an implicit solvent pro-vides the similar result (HPAI complex has higher activity than LPAI for both systems) in characterization of pathogenic virus neuramini-dase activity.