RNA is a key participant in many
biological processes, but studies
of RNA using computer simulations lag behind those of proteins, largely
due to less-developed force fields and the slow dynamics of RNA. Generating
converged RNA ensembles for force field development and other studies
remains a challenge. In this study, we explore the ability of replica
exchange molecular dynamics to obtain well-converged conformational
ensembles for two RNA hairpin systems in an implicit solvent. Even
for these small model systems, standard REMD remains computationally
costly, but coupling to a pre-generated structure library using the
reservoir REMD approach provides a dramatic acceleration of ensemble
convergence for both model systems. Such precise ensembles could facilitate
RNA force field development and validation and applications of simulation
to more complex RNA systems. The advantages and remaining challenges
of applying R-REMD to RNA are investigated in detail.
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