CHAPTER 8: In Silico Approaches to Design and Characterize Peptide-based Nanostructures

Molecular dynamics (MD) simulations can show structural and dynamic details on an atomistic level in a native-like environment. Conventional atomistic MD simulations have been successfully applied to many problems, however, they often do not cover the necessary timescales to sufficiently explore conformational phase and reach convergence. In this study, we discuss two examples where we have employed atomistic simulations followed by either Hamiltonian replica exchange molecular dynamics (H-REMD) or coarse-grained (CG) simulations to identify the intrinsic details of nanostructure formation processes and the influence of various factors on them. We demonstrate that combining computational approaches or resolution levels is very useful to overcome the limitations of a single method, like pure atomistic simulations, while still keeping its advantages. However, it is very important to carefully select suitable methods, parameters and approaches to get meaningful results with sufficient accuracy.