Variable-Scale Coarse-Graining in Macromolecular Global Optimization

We discuss the use of variable-scale coarse-graining for global minimization of macromolecular energy functions and compare three related methods. The Diffusion Equation Method and Adiabatic Gaussian Density Annealing are briefly reviewed and our Packet Annealing Method is discussed in more detail. All three methods dissect the global minimization problem into a sequence of local minimization problems on smoothed objective functions. They differ in the use of either energy averaging or free-energy averaging, the degree of anisotropy allowed in the objective function smoothing, and in tracking either single or multiple trajectories during the annealing procedure. Energy landscape scaling properties, which characterize the suitability of a potential landscape for this type of approach, are are also discussed.

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