Introducing the effective polarizable bond (EPB) model in DNA simulations

Abstract

Electrostatic polarization plays an important role in characterizing non-bonded interactions of molecule dynamics (MD) simulation of biomolecules. In this work, we extended a simple fluctuating-charge model, the effective polarizable bond (EPB) model to DNA simulations. Following the previously proposed EPB method, we re-parametrized the EPB model for DNA systems with the consideration of a realistic local electric-field environment and derived a set of DNA-specific EPB parameters. Two typical B-DNA systems, a pure DNA 1BNA and a ligand-DNA 8BNA systems were simulated respectively in the ff14SB and ff14SBEPB force fields. Results demonstrate that use of the EPB model in the DNA simulations can cause shrinking of DNA double strands along central axis and strengthen base-pair/ligand-DNA hydrogen-bond (HB) interactions. Furthermore, it stabilizes residue-level fluctuations for the 1BNA. However, it is largely different for these two DNA systems to mimic conformation changes of the minor/major grooves by the EPB model. Lastly, it is tested that approximately %9∼%9.9 CPU costs are additionally taken to execute the EPB calculations compared with the conventional ff14SB force field.