Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation.

Abstract

The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental force spectroscopy, often coarse graining procedures are employed. Here, building on a previous study, we apply the adaptive resolution scheme (AdResS) to force probe molecular dynamics (FPMD) simulations using two model systems as examples: One system is the previously investigated calix[4]arene dimer that shows reversible one-step unfolding, and the other example is provided by a small peptide, a β-alanine octamer in methanol solvent. The mechanical unfolding of this peptide proceeds via a metastable intermediate and, therefore, represents a first step toward a complex unfolding pathway. We show that the average number of native contacts serves as a robust order parameter for the forced unfolding of this small peptide. In addition to increasing the complexity of the relevant conformational changes, we study the impact of the methodology used for coarse graining. Apart from the iterative Boltzmann inversion method, we apply an ideal gas approximation, and therefore, we replace the solvent by a non-interacting system of spherical particles. In all cases, we find excellent agreement between the results of FPMD simulations performed fully atomistically and those of the AdResS simulations also in the case of fast pulling. This holds for all details of the unfolding pathways, such as the distributions of the characteristic forces and also the sequence of hydrogen-bond opening in case of the β-alanine octamer. Therefore, the methodology is very well suited to simulate the mechanical unfolding of systems of experimental relevance.