Theoretical Chemistry Accounts

, Volume 99, Issue 5, pp 279–288

Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution

  • Thomas E. Cheatham III.
  • Bernard R. Brooks

DOI: 10.1007/s002140050337

Cite this article as:
Cheatham III., T. & Brooks, B. Theor Chem Acc (1998) 99: 279. doi:10.1007/s002140050337


Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared deviations from experimental structures and now provide believable structural insight into a variety of processes such as the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald methods are becoming the de facto standard.

Key words: Molecular dynamics Biomolecular simulation 

Copyright information

© Springer-Verlag Berlin Heidelberg 1998

Authors and Affiliations

  • Thomas E. Cheatham III.
    • 1
  • Bernard R. Brooks
    • 1
  1. 1.Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, 12A-2041, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892-5626, USAUS

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