We present results of molecular dynamics simulations performed using a multi-purpose computer codeMBN Explorer. In particular we consider the process of laser induced acoustic desorption of lysine amino acids from the surface of a nickel foil. We analyze the rate of lysine desorption from the nickel foil at different foil accelerations and suggest a simple theoretical model to describe the observed results. We note that despite the universality the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes.