Implicit Solvation ParametersDerived from ExplicitWater Forces in Large-Scale Molecular Dynamics Simulations

摘要

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 σi^SASA. A procedure for the determination of values for the σi^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 σi^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 σg^SASA was obtained via partitioning of the atom–type σi^SASA distributions by dynamic programming.Three groups of atom types with well separated parameter ranges wereobtained, and their performance in implicit versus explicit simulationswas assessed. The solvent forces are available at .