Molecular Dynamics (MD) simulations allow us to observe the time-dependent behavior of molecular systems at an atomic level. Unlike static docking models, MD simulations provide a detailed look at the flexibility and conformational changes that occur as host and guest molecules interact in a solvent environment.

By solving Newton’s equations of motion for a system of interacting particles, we can calculate trajectories that reveal the stability of various complexes over nanosecond or microsecond timescales. In our group, @Sofia Moco and others use #MD simulations to study the equilibrium between bound and unbound states, as well as the pathways by which molecules enter and exit host cavities. Recent advancements in force field parameters and hardware acceleration have significantly expanded our ability to model large-scale biological systems and synthetic macrocycles with high precision.