Multiple molecular dynamics simulations of the anticodon loop of tRNA(super Asp) in aqueous solution with counterions

A nanosecond of molecular dynamics (MD) simulation on the solvated anticodon loop of tRNA(super Asp) is analyzed, directing to address the ramifications of the detected differences in ten 100 ps molecular dynamics trajectories produced by modifying initial protocol of the systems. The resulting divergent trajectories differ in structural and dynamical characteristics. No relation exists between the modifications made in the system and the properties of the trajectories. The multiple MD recognized the protocol stability.