STRUCTURE OPTIMIZATION COMBINING SOFT-CORE INTERACTION FUNCTIONS, THEDIFFUSION EQUATION METHOD, AND MOLECULAR-DYNAMICS

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of so ft-core potential energy functions and a variation of the diffusion eq uation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simu lations were repeated many times using different initial conditions an d structures since the methods are heuristic and results are only mean ingful in a statistical sense.