Martini Force Field for Protonated Polyethyleneimine.

Polyethyleneimine (PEI), one of the most widely used nonviral gene carriers, was investigated in the presented work at coarse-grained (CG) level. The main focus was on elaborating a realistic CG force field (FF) aimed to reproduce dynamic structural features of protonated PEI chains and, furthermore, to enable massive simulations of DNA-PEI complex formation and condensation. We parametrized CG Martini FF models for PEI in polarizable and nonpolarizable water by applying Boltzmann inversion techniques to all-atom (AA) probability distributions for distances, angles, and dihedrals of entire monomers. The fine-tuning of the FFs was achieved by fitting simulated CG gyration radii and end-to-end distances to their AA counterparts. The developed Martini FF models are shown to be well suited for realistic large-scale simulations of size/protonation-dependent behavior of solvated PEI chains, either individually or as part of DNA-PEI systems. © 2019 Wiley Periodicals, Inc.