Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes
Na Li, Ya Gao, Feng Qiu, Tong Zhu
Abstract
G-quadruplexes have drawn widespread attention for serving as a potential anti-cancer target and their application in material science. Molecular dynamics (MD) simulation is the key theoretical tool in the study of GQ's structure-function relationship. In this article, we systematically benchmarked the five force fields of parmbsc0, parmbsc1, OL15, AMOEBA, and Drude2017 on the MD simulation of G-quadruplex from four aspects: structural stability, central ion channel stability, description of Hoogsteen hydrogen bond network, and description of the main chain dihedral angle. The results show that the overall performance of the Drude force field is the best. Although there may be a certain over-polarization effect, it is still the best choice for the MD simulation of G-quadruplexes.