Simulated annealing Conformation search

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

Quenched dynamics can trap structures in local minima. To prevent this problem, you can cool the system slowly to room temperature or some appropriate lower temperature. Then run room temperature molecular dynamics simulations to search for conformations that have lower energies, closer to the starting structure. Cooling a structure slowly is called simulated annealing. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

This criterion requires a search through a nonconvex multidimensional conformation space that contains an immense number of minima. Optimization techniques that have been applied to the problem include Monte Carlo methods, simulated annealing, genetic methods, and stochastic search, among others. For reviews of the application of various optimization methods refer to Pardalos et al. (1996), Vasquez et al. (1994), or Schlick et al. (1999). 

Simulated annealing to be used in conjunction with MULTIC conformational search routine of MacroModel. 

The goal of any optimization problem is to find the global minimum of a target function. In the case of crystallographic refinement, one searches for the conformation or conformations of the molecule that best fit the diffraction data at the same time that they maintain reasonable covalent and non-covalent interactions. As the above examples have shown, simulated annealing refinement has a much larger radius of convergence than... 

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