Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short Molecular Dynamics (MD) simulations, such as MM-PBSA and MM-GBSA, among generated docking poses have been used. Since molecular structures obtained from MD simulation depend on the initial condition, taking the average over different initial conditions leads to better accuracy. Prediction accuracy of protein-ligand binding poses can be improved with multiple runs at different initial velocity.