Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …

In the last five years we have witnessed a significant increase in the number publications
describing accurate and reliable all‐atom molecular dynamics simulations of nucleic acids …

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐
spline interpolation of the structure factors. This reformulation allows a natural extension of …

Publisher Summary This chapter discusses the structure and function of DNA. DNA occupies
a critical role in cells, because it is the source of all intrinsic genetic information. Chemically …

We have examined some subtle parameter modifications to the Cornell et al. force field,
which has proven quite successful in reproducing nucleic acid properties, but whose C2 …

Molecular dynamics simulations based on empirical force fields can greatly enhance
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …

We review molecular dynamics simulations of nucleic acids, including those completed from
1995 to 2000, with a focus on the applications and results rather than the methods. After the …

The dynamics, hydration, and ion-binding features of two duplexes, the A (r (CG) 12) and the
B (d (CG) 12), in a neutralizing aqueous environment with 0.25 M added KCl have been …

Nanosecond length simulations applying the particle mesh Ewald method within AMBER 4.1
on canonical A-form and B-form geometries of d [CCAACGTTGG] 2, r [CCAACGUUGG] 2 …

Long-range interactions are known to play an important role in highly polar biomolecules
like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate …