The structure and dynamics of various atoms of the most common primary structure in heteropoly compounds, namely the Keggin structure were analyzed by molecular dynamics (MD), The atoms in the primary structure were found to remain rigid at 300 K, The study was also extended to understand the dynamics of the secondary structures, namely the countercations and the water molecules which are located between heteropolyanions, The smaller countercations such as Li+ and Na+ were relatively more mobile than the larger cations such as K+ and Cs+, The water molecules were mobile as in the bulk liquid phase water, A quantitative estimate of the relative mobility of primary and secondary structure of 12-heteropoly compounds in terms of mean square displacement, which are important in relation to their catalytic properties, were reported.