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

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 ff14SB^EPB 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.