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Exploring the similarities between potential smoothing and simulated annealing

✍ Scribed by Hart, Reece K.; Pappu, Rohit V.; Ponder, Jay W.

Publisher
John Wiley and Sons
Year
2000
Tongue
English
Weight
438 KB
Volume
21
Category
Article
ISSN
0192-8651

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✦ Synopsis

Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as implemented in the diffusion equation method has been applied to study partitioning of the potential energy surface (PES) for N-Acetyl-Ala-Ala-N-Methylamide (CDAP) and the clustering of conformations on deformed surfaces. A deformable version of the united-atom OPLS force field is described, and used to locate all local minima and conformational transition states on the CDAP surface. It is shown that the smoothing process clusters conformations in a manner consistent with the inherent structure of the undeformed PES. Smoothing deforms the original surface in three ways: structural shifting of individual minima, merging of adjacent minima, and energy crossings between unrelated minima. A master equation approach and explicit molecular dynamics trajectories are used to uncover similar features in the equilibrium probability distribution of CDAP minima as a function of temperature. Qualitative and quantitative correlations between the simulated annealing and potential smoothing approaches to enhanced conformational sampling are established.

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