期刊
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
卷 1850, 期 5, 页码 861-871出版社
ELSEVIER SCIENCE BV
DOI: 10.1016/j.bbagen.2014.08.004
关键词
Molecular dynamics; Empirical force field; Potential energy function; Molecular Mechanics; Computer-aided drug design; Biophysics
资金
- NIH [GM051501, GM070855, GM072558]
- NSF [CHE-0823198]
- Waxman Foundation
- University of Maryland Computer-Aided Drug Design Center
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [0823198] Funding Source: National Science Foundation
Background: Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of review: As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular biomolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields' parametrization philosophy and methodology. Major conclusions: Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 mu s on proteins, DNA, lipids and carbohydrates. General significance: Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. This article is part of a Special Issue entitled Recent developments of molecular dynamics. (C) 2014 Elsevier B.V. All rights reserved.
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