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

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 σiSASA. A procedure
for the determination of values for the σiSASA 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 σiSASA 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 σgSASA was
obtained via partitioning of the atom–type
σiSASA 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.