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Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.
MedLine Citation:
PMID:  23180979     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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-solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom-specific solvation parameter σ(i) (SASA). A procedure for the determination of values for the σ(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 σ(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 σ(g) (SASA) was obtained via partitioning of the atom-type σ(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.
Authors:
Jens Kleinjung; Walter R P Scott; Jane R Allison; Wilfred F van Gunsteren; Franca Fraternali
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-6-12
Journal Detail:
Title:  Journal of chemical theory and computation     Volume:  8     ISSN:  1549-9626     ISO Abbreviation:  J Chem Theory Comput     Publication Date:  2012 Jul 
Date Detail:
Created Date:  2012-11-27     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101232704     Medline TA:  J Chem Theory Comput     Country:  -    
Other Details:
Languages:  ENG     Pagination:  2391-2403     Citation Subset:  -    
Affiliation:
Division of Mathematical Biology, MRC National Institute for Medical Research , The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom.
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