Simulated annealing procedure

Floquet, P. L. Pibouleau and S. Domenech. Separation Sequence Synthesis How to Use a Simulated Annealing Procedure Comput Chemung 18 1141-1148 (1994). 

Since the energy landscape of a simulated annealing procedure in which only dipolar couplings are included tends to have many local minima, these orientational restraints are usually introduced once a preliminary structure has been calculated from NOE data. This procedure has also the advantage of identifying misassigned NOEs and possible conflicts among the various types of input data. 

In the most general case of a completely anisotropic diffusion tensor, six parameters have to be determined for the rotational diffusion tensor three principal values and three Euler angles. This determination requires an optimization search in a six-dimensional space, which could be a significantly more CPU-demanding procedure than that for an axially symmetric tensor. Possible efficient approaches to this problem suggested recently include a simulated annealing procedure [54] and a two-step procedure [55]. 

Takashima et aln designed a multiplied simulated annealing procedure (Fig. 4) to implement distributed computing for protein structure determination, and applied it to a P-sheet-rich protein neocarzinostatin (113 amino acids + chromophore). The procedure consists of the higher and lower initial... 

Fig. 4. Calculation regimen of a multiplied simulated annealing procedure. The number of structures is indicated by parenthesis. All simulated annealing (SA) were restrained by NMR-derived information.

It is possible to use an alternative approach, regarding the minimization of the functional as an optimization problem, which can be solved by means of the simulated annealing procedure. A simulated annealing technique based on MD can be efficiently applied to minimize the KS functional the resulting technique, called dynamical simulated annealing allows the study of finite temperature properties. 

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