In a systematic search for a stable protocol with which to extend our dynamical investigations, a nanosecond of molecular dynamics simulations of the solvated anticodon loop of tRNA(Asp) consisting of ten unique trajectories was obtained by slight modifications to the starting conditions. These changes produced divergent trajectories which varied widely in structural and dynamical characteristics. However, the properties of these trajectories could not be directly correlated to the slight modifications introduced in the system, and thus, questions were raised regarding the probity of the standard protocol we utilized. Instead of a detailed analysis of the results, the multiple molecular dynamics (MD) approach was used as a diagnostic for estimating the reliability of the set of trajectories generated and the extent of relevant biochemical information which can be extracted from it. We address here issues concerning critical evaluation of molecular dynamics methodology and detection of protocol instabilities. We infer that an ensemble of initial uncorrelated trajectories should be generated in order to investigate the constancy of structural and dynamical properties of the system under study.