RECENT ADVANCES IN MOLECULAR-DYNAMICS SIMULATION TOWARDS THE REALISTIC REPRESENTATION OF BIOMOLECULES IN SOLUTION

Coupled advances in empirical force fields and classical molecular dyn amics simulation methodologies, combined with the availability of fast er computers, has lead to significant progress towards accurately repr esenting the structure and dynamics of biomolecular systems, such as p roteins, nucleic acids, and lipids in their native environments. Thank s to these advances, simulation results are moving beyond merely evalu ating force fields, displaying expected structural fluctuations, or de monstrating low root-mean-squared deviations from experimental structu res and now provide believable structural insight into a variety of pr ocesses such as the stabilization of A-DNA in mixed water and ethanol solution or reversible beta-peptide folding in methanol. The purpose o f this overview is to take stock of these recent advances in biomolecu lar simulation and point out some common deficiencies exposed in longe r simulations. The most significant methodological advances relate to the development of fast methods to properly treat long-range electrost atic interactions, and in this regard the fast Ewald methods are becom ing the de facto standard.