Observations on the a versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA

Molecular dynamics simulations of duplex DNA or RNA in solution now yield stable structures for a duration of well over 1 ns. Different force fields, however, lead to different equilibrium structures. Presented are details of the equilibrium between the A and B forms of DNA by the CHARMM all-hydrogen force field for several sequences, including previously unpublished results on the d[GCGCGCG](2) and d[ATATATA](2) duplexes in solution. Comments ale also included on the performance of other fold fields. Based on a combination of observations a dominate role of the sugar and phosphodiester backbone moieties in the equilibrium between the A and B forms of DNA is suggested.