Molecular Dynamics Simulations as a Complement to Nuclear Magnetic Resonance and X-Ray Diffraction Measurements

Abstract

Advances in the field of atomic-level membrane simulations are being driven by continued growth in computing power, improvements in the available potential energy functions for lipids, and new algorithms that implement advanced sampling techniques. These developments are allowing simulations to assess time- and length scales wherein meaningful comparisons with experimental measurements on macroscopic systems can be made. Such comparisons provide stringent tests of the simulation methodologies and force fields, and thus, advance the simulation field by pointing out shortcomings of the models. Extensive testing against available experimental data suggests that for many properties modern simulations have achieved a level of accuracy that provides substantial predictive power and can aid in the interpretation of experimental data. This combination of closely coupled laboratory experiments and molecular dynamics simulations holds great promise for the understanding of membrane systems. In the following, the molecular dynamics method is described with particular attention to those aspects critical for simulating membrane systems and to the calculation of experimental observables from the simulation trajectory.