Molecular Dynamics of Biomolecules

Abstract

To fulfill their biological function, proteins and nucleic acids undergo preci-se conformational changes. These changes are brought about by the coordination of small fluctuations executed by their atoms. Interestingly, at first glance, these atoms seem to move in a chaotic manner. Molecular dynamics simulations (MD) are a particularly versatile tool for investigating the connection between quasi-random atomic motions and conformational changes. In this way, they allow us to build bridges from sequence to structure, and from there to dynamics and biological function.
The fundamentals of MD simulations are simple and intuitive. However, when implementing a specific study, it is possible to make many poor decisions that will not prevent the calculation from being performed but will surreptitiously render its results devoid of any value. In this article, we will present the fundamental concepts of MD simulations, highlighting those aspects that are critical to ensuring their utility. Additionally, we will discuss their strengths and limitations, emphasizing how they have evolved over time. Furthermore, we will provide paradigmatic examples that illustrate the current capabilities of this valuable computational tool.