MD simulations were performed to sample conformational space of complexes between neuraminidase and ligands in aqueous solution. Amber99SB-iLDN force field was employed to parameterized inter-atomic interactions of the protein and counter ions. For water molecules, TIP3P water model was used. The general Amber force field (GAFF) was employed for Lennard Jones and bonded interactions for the ligand. AmberTools18 and ACPYPE packages was applied to fit the point charges of the ligand using the restrained electrostatic potential (RESP) method electrostatic potential grid which was calculated by DFT based on the double hybrid functional Mp2, basis set 6-31G(d,p), and implicit solvent (𝜀 = 78.4). The neuraminidase-ligand complexes were inserted into a water box with dodecahedral periodic boundary conditions. The box size was chosen such that there was a minimum distance of 16.0 Å between the protein-ligand complex and the box edge. The box had a volume of 569.75 nm and contained in total 56000 atoms. The water box for MD simulations of free ligands had a volume of 56.16 nm and a total number of atoms of 5500.