Simulations of the B‐DNA molecular dynamics of d(CGCGAATTCGCG) 2 and d(GCGCGCGCGC) 2 : An analysis of the role of initial geometry and a comparison of united and all‐atom models

Abstract Molecular dynamics simulations on the sequence d(CGCGAATTCGCG) 2 have been carried out using both united atom and all‐atom representations, and starting the simulations both from a regular repeating B‐DNA structure and from the x‐ray single crystal B‐DNA structure. An all‐atom B‐DNA simulation on the sequence d(GCGCGCGCGC) 2 has also been carried out, in order to compare it with a previous united atom simulation. The helix repeats, H‐bonding, sugar pucker profiles, and average torsional angles are all in the range observed in crystallographic and nmr studies for B‐DNA helices. In some of the sequences, there is a significant bend in the DNA helices. The individual helix repeats, with focus on 3′CpG5′ and 3′GpC5′ units, show the opposite helix repeat to that suggested by Calladine's rules.