Refining a Model with Molecular Dynamics

Molecular dynamics (MD), while computationally very expensive, is often used to relax structures, relieve local strain, and refine models of macro-molecular structures or complexes of these with ligands docked into the receptor site. Basically, MD consists of solving Newton s equations of motion for each atom in a system as a function of time and energy funaions describing interatomic forces. While calculating the atomic trajeaories is slow, once calculated these can be stored and often played back in real time, thus creating a picture of the system as it evolves over time. 

MD is particularly useful in macromolecular systems, where conformational search is impractical. -i°3 yhe nonbonded cutoffs,the temperature 

---