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A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
Oostenbrink, C., Villa, A., Mark, A. E. and Van Gunsteren, W. F. (2004-10) A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25 13: 1656-1676.
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| Author(s) |
Oostenbrink, C.
Villa, A.
Mark, A. E.
Van Gunsteren, W. F.
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| Title |
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
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| Journal name |
Journal of Computational Chemistry
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| Publication date |
2004-10
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| Year available |
2004
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| Volume number |
25
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| Issue number |
13
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| ISSN |
0192-8651
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| Start page |
1656
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| End page |
1676
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| Total pages |
21
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| Place of publication |
Hoboken
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| Publisher |
John Wiley & Sons Inc
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| Language |
eng
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| Abstract |
Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed. (C) 2004 Wiley Periodicals, Inc.
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| Keyword(s) |
Chemistry, Multidisciplinary
GROMOS force field
force-field parameterization
free-energy calculation
solvation
hydration
Molecular-dynamics Simulations
Free-energy Calculations
Human Alpha-lactalbumin
Side-chain Analogs
Computer-simulation
Nucleic-acids
N-alkanes
Thermodynamic Properties
Conformational Dynamics
Dimethyl-sulfoxide
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