Dependence of A-RNA simulations on the choice of the force field and salt strength†
Abstract
We present an extensive molecular dynamics study (0.6 μs in total) on three A-RNA duplexes. The dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions (∼0.18 M net-neutralizing Na+ and ∼0.3 M KCl) was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary α/γ t/t flips common in Parm99 simulations. Nevertheless, since the α/γ t/t sub-state occurs to certain extent in experimental A-RNA structures, we consider both force fields as viable. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible
- This article is part of the themed collection: Nucleic acid simulations