Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA
1998
MacKerell, A.D. Jr
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between the A and B forms of DNA by the CHARMM all-hydrogen force field for several sequences, including previously unpublished results on the d[GCGCGCG]2 and d[ATATATA]2 duplexes in solution Comments are also included on the performance of other force fields.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.
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