Using Blue Waters Petascale resources for atomistic molecular dynamics simulations of various nucleic acid systems alone and interacting with various ligands and proteins we have been able to effectively demonstrate "convergence" and "reproducibility" in the results. This is enabled by optimized versions of AMBER on GPU resources and ensemble-based replica-exchange molecular dynamics simulations. Although truly defining "convergence" is elusive, we demonstrate that independent sets of simulations with vastly different initial conditions and even different enhanced sampling methods give conformational ensembles that are essentially indistiguishable from each other. Convergence has been shown for internal DNA helices, RNA tetranucleotides, RNA tetraloops, and other systems. The effective sampling provides an excellent means to validate and assess force fields. Shared data resulting, specifically ensembles of converged RNA simulations, will ultimately be made available using the new data sharing services on Blue Waters.
