Simulated annealing simulation length

Fig. 3.1. The cooling schedule during a simulated annealing run of 106 MC steps with goal curvature c0 = 10 in a box of unit edge length. The temperature program corresponds to a = 3. The adaptive changes in 6

Santos [98] carried out the simulated annealing simulation on DEC 8400 machines. For the model system comprising 173 (N = 8) Fourier modes and 233 test points in a simulation box, on average 16 MC steps per second could be performed. The length of the runs extends from 2 106 to 5 106 MC steps. 

Monte Carlo/simulated annealing (MC/SA) algorithm for sequential assignment in uniformly 13C, 15N-labeled proteins [137]. The two-dimensional (2D) NCACX and NCOCX spectra measured for the fibril samples of full-length Syrian hamster prion protein (residues 23-231) have been analyzed by the MC/SA protocol, from which it has been concluded that the fibril core is formed primarily in the region of residues 173-224 [54]. 

Note that R drops precipitously in the first stages of refinement after ALBP side chains replace those of P2. Note also that R and the deviations from ideal bond lengths, bond angles, and planarity of peptide bonds decline smoothly throughout the later stages of refinement. The small increase in R at the end is due to inclusion of weaker reflections in the final round of simulated annealing. 

Fig. 30. Energy distribution of the spin system as obtained from randomly generated sequences of length 1024 and 16384 and after 1-spin-flip optimization with and without simulated annealing...

The optimization is accomplished through a simulated annealing engine with cost function given by Equation (5.1). The cost function is the weighted sum of three components total wire length, floorplan area, and total number of inter-chip contacts. 

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