A new simulated annealing method combined with a polarizable continuum model based on the boundary element method

We propose a novel combined method of a polarizable continuum model and molecular dynamics simulation. In this method, a solute–solvent interaction force is obtained by solving the Poisson equation of a system with the aid of the so-called boundary element method. From a 4 ns simulation for the aqueous solution of alanine dipeptide (N-acetylalanyl-N′-methylamide), it is confirmed that the calculation can provide the thermodynamically correct picture about the conformational distributions of the ϕ and ψ angles. The results of several simulated annealing runs indicate that the method is available for finding the global minimum conformation of molecules in water.