Simple method for Hybrid All-Atom and Coarse-Grained Molecular Dynamics Simulations and Its Applications

Abstract

Hybrid all-atom (AA) and coarse-grained (CG) simulation has the possibility of overcoming the limitations of both AA and CG molecular dynamics (MD) simulations. HybridAA/CGsystems are practicable to simulatemicrosecond timescale and to get detailed information formolecular structures.Many existingmethods for hybrid AA/CG simulations tend to require heavy parameterizations that complicate multiscale simulations. We test a simple scheme for simulating hybrid AA/ CG systems using standard AA and CG force fields, together with four small proteins as test cases for the scheme.Our method uses virtual sites for interactions betweenCGandAAresolution as reported earlier (Rzepiela et al.Phys.Chem.Chem. Phys. 2011, 13, 10437-10448) and we add distance restrained FG water layer to improve the reliability of the hybrid simulation. We observe that the addition of distance restrained FG water layer in the hybrid simulation results in close accord with the structure from the atomistic simulations. However, there are also digressions fromcorrect behaviors that need to be addressed in future developments.We show such various results in detail and discuss the prospects of our scheme.