Molecular dynamics simulations are a powerful tool for analyzing the motions and energetics of large biological molecules, which are dynamic entities in constant motion under physiological conditions. These simulations address the challenges of assessing the stability and function of proteins, nucleic acids, and other biomolecules by using detailed physical models that describe the energy of molecular conformations and integrating the equations of motion to produce movies of molecular motion. The potential energy functions used in these simulations include terms for bond interactions and long-range interactions such as van der Waals and electrostatic forces. The simulations often start with high-resolution structures from X-ray crystallography or NMR studies, and the initial portion is an equilibration period that is discarded, leaving the 'production dynamics' period for detailed analysis. Recent improvements in simulation techniques include more accurate parameter sets, methods for handling multiple time scales, efficient computation of long-range interactions, and global optimization techniques. These advancements have made molecular dynamics simulations accessible to a broad range of scientists and have significantly enhanced their efficiency, accuracy, and applicability in various biological research areas, including protein folding, signal transduction, and drug design.Molecular dynamics simulations are a powerful tool for analyzing the motions and energetics of large biological molecules, which are dynamic entities in constant motion under physiological conditions. These simulations address the challenges of assessing the stability and function of proteins, nucleic acids, and other biomolecules by using detailed physical models that describe the energy of molecular conformations and integrating the equations of motion to produce movies of molecular motion. The potential energy functions used in these simulations include terms for bond interactions and long-range interactions such as van der Waals and electrostatic forces. The simulations often start with high-resolution structures from X-ray crystallography or NMR studies, and the initial portion is an equilibration period that is discarded, leaving the 'production dynamics' period for detailed analysis. Recent improvements in simulation techniques include more accurate parameter sets, methods for handling multiple time scales, efficient computation of long-range interactions, and global optimization techniques. These advancements have made molecular dynamics simulations accessible to a broad range of scientists and have significantly enhanced their efficiency, accuracy, and applicability in various biological research areas, including protein folding, signal transduction, and drug design.