Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

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• 作者：Jens Kleinjung ; Walter R. P. Scott ; Jane R. Allison ; Wilfred F. van Gunsteren ; Franca Fraternali
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2012
• 出版时间：July 10, 2012
• 年：2012
• 卷：8
• 期：7
• 页码：2391-2403
• 全文大小：787K
• 年卷期：v.8,no.7(July 10, 2012)
• ISSN：1549-9626

文摘

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent鈥搒olute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom鈥搒pecific solvation parameter 蟽_i^SASA. A procedure for the determination of values for the 蟽_i^SASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the 蟽_i^SASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types 蟽_g^SASA was obtained via partitioning of the atom鈥搕ype 蟽_i^SASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces.