MULTIPLE MOLECULAR-DYNAMICS SIMULATIONS OF THE ANTICODON LOOP OF TRNA(ASP) IN AQUEOUS-SOLUTION WITH COUNTERIONS

In a systematic search for a stable protocol with which to extend our dynamical investigations, a nanosecond of molecular dynamics simulatio ns of the solvated anticodon loop of tRNA(Asp) consisting of ten uniqu e trajectories was obtained by slight modifications to the starting co nditions. These changes produced divergent trajectories which varied w idely in structural and dynamical characteristics. However, the proper ties of these trajectories could not be directly correlated to the sli ght modifications introduced in the system, and thus, questions were r aised regarding the probity of the standard protocol we utilized. Inst ead of a detailed analysis of the results, the multiple molecular dyna mics (MD) approach was used as a diagnostic for estimating the reliabi lity of the set of trajectories generated and the extent of relevant b iochemical information which can be extracted from it. We address here issues concerning critical evaluation of molecular dynamics methodolo gy and detection of protocol instabilities. We infer that an ensemble of initial uncorrelated trajectories should be generated in order to i nvestigate the constancy of structural and dynamical properties of the system under study.