Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.

ABSTRACT: Molecular dynamics (MD) simulations play a crucial role in modeling biomolecular systems in which the electrostatic interactions are critical in dictating the structural and dynamical properties. Thus, the treatment of the electrostatic interactions defined in the underlying force field (FF) strongly affects the simulation accuracy. Most FFs use fixed partial atomic charges to include electrostatic interactions, and therefore lack the electronic polarization response, representing an intrinsic limitation. To address this limitation, polarizable FFs have been developed that treat atomic polarizabilities explicitly. Here we present the application of the all-atom polarizable (Drude) and non-polarizable (CHARMM) nucleic acid FFs in RNA hairpin systems to investigate the impact of polarization

SUBMITTER: Sengul MY 

PROVIDER: S-EPMC9231828 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature