Structural Biology

Molecular Modelling and Dynamics

Molecular modeling involves hypothetical and computational procedures used to mimic the behavior of macromolecules. These techniques are applied in various fields such as drug design, computational chemistry, materials science, and computational biology. They help in studying and understanding the structural and functional properties of molecules. One of the major applications of molecular modeling is molecular simulation, which uses powerful computers to simulate interactions between atoms and explore the properties of materials. Such simulations range from highly detailed quantum mechanical calculations at the atomic level to coarse-grained classical dynamics of large molecular systems over timescales of milliseconds or longer.

Molecular dynamics (MD) specifically focuses on studying the physical movements of atoms and molecules using simulation techniques, and is classified as a type of N-body simulation. Atoms and molecules are allowed to interact over a fixed time period, providing insight into the dynamic evolution of the system. Their trajectories are typically determined by numerically solving Newton’s equations of motion for groups of interacting particles. The forces and potential energies are calculated using interatomic potentials or molecular mechanics force fields. An extension of this method, Steered Molecular Dynamics (SMD), allows researchers to apply external forces to simulate mechanical unfolding or molecular recognition processes in a more targeted manner.