Classical molecular dynamics simulations of hydrogen plasmas have been performed with an emphasis on the analysis of the equilibration process. The theoretical basis of the simulation model as well as numerically relevant aspects, such as the proper choice and definition of simulation units, are discussed in detail, thus proving a thorough implementation of the computer simulation technique. Because of the lack of experimental data, molecular dynamics simulations are often considered as idealized computational experiments for benchmarking of theoretical models. However, these simulations are certainly challenging and consequently a validation procedure is also demanded. In this work we develop an analytical statistical equilibrium model for computational validity assessment of plasma particle dynamics simulations. Remarkable agreement between model and molecular dynamics results including a classical treatment of the ionization-recombination mechanism is obtained for a wide range of plasma coupling parameter values. Furthermore, the analytical model provides guidance to securely terminate simulation runs once the equilibrium stage has been reached, which in turn gives confidence in the statistics that potentially may be extracted from time histories of simulated physical quantities.