Molecular Dynamics Simulations of Biomolecules
نویسندگان
چکیده
منابع مشابه
Coarse-grained molecular dynamics simulations of biomolecules
Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances...
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Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulat...
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Biological molecules are highly dynamic and coexist in multiple conformations in solution [1]. Molecular motions are observed on a broad range of time and length scales using spectroscopy and hydrogen–deuterium exchange experiments [2–5]. The internal motions and resulting conformational changes of these molecules play an essential role in their function. Sampling the structural and dynamic pro...
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Properties of biomolecules are often investigated using Molecular Dynamics (MD) simulations whereby atoms and molecules interact for a period of time, thus revealing the time dependent behavior of the system. Whereas the atom positions of the starting structures for such MD runs are usually derived from X-ray crystallography or NMR experiments, properties such as charges or bonds are specified ...
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Due to the very long timescales involved (µs−s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programming platform to the more traditional CPUs as th...
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ژورنال
عنوان ژورنال: Accounts of Chemical Research
سال: 2002
ISSN: 0001-4842,1520-4898
DOI: 10.1021/ar020082r