Ab initio molecular dynamics of fully solvated biomolecules with periodic boundary conditions using the Oak Ridge Leadership Computing Facility (OLCF) supercomputers

We present the first nanosecond-scale molecular dynamics simulations of small ribonucleic acids with a full solvation shell of explicit water and ions at the density functional theory (DFT) level, using high performance ab initio molecular dynamics programs and the OLCF supercomputers. Comparison of the trajectories to classical molecular dynamics performed, including effects of polarization, changes in molecular conformations, and dynamics of the system in metastable states and with respect to barrier crossing. We find important differences in the conformational dynamics that can be attributed to effects of dynamic changes to polarization and which may be essential to a correct description of conformational ensembles of these difficult to model molecules.