Discrete Molecular Dynamics Simulation of Biomolecules

Abstract

Biological molecules are highly dynamic and coexist in multiple conformations in solution [1]. Molecular motions are observed on a broad range of time and length scales using spectroscopy and hydrogen–deuterium exchange experiments [2, 3, 4, 5]. The internal motions and resulting conformational changes of these molecules play an essential role in their function. Sampling the structural and dynamic properties of biomolecules remains a challenge due to the large range of time and length scales associated with molecular life. Molecular modeling, especially molecular dynamics simulations of biomolecules and molecular complexes, has played a crucial role in bridging time and length scale gaps and has been pivotal to our understanding of the dynamic aspect of biomolecules[6].