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A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin
Author(s) -
Nayeem Akbar,
Vila Jorge,
Scheraga Harold A.
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120509
Subject(s) - maxima and minima , monte carlo method , simulated annealing , statistical physics , energy minimization , energy landscape , potential energy , molecular dynamics , minification , mathematics , space (punctuation) , global optimization , chemistry , physics , mathematical optimization , computer science , computational chemistry , thermodynamics , mathematical analysis , classical mechanics , statistics , operating system
Abstract A comparison of two methods for surmounting the multiple‐minima problem, Simulated Annealing (SA) and Monte Carlo with Minimization (MCM), is presented with applications to [Met]‐enkephalin in the absence and in the presence of water. SA explores a continuous space of internal variables, while MCM explores a discrete space consisting of the local energy minima on that space. Starting from random conformations chosen from the whole conformational space in both cases, it is found that, while SA converges to low‐energy structures significantly faster than MCM, the former does not converge to a unique minimum whereas the latter does. Furthermore, the behavior of the RMS deviations with respect to the apparent global minimum (for enkephalin in the absence of water) shows no correlation with the observed overall energy decrease in the case of SA, whereas such a correlation is quite evident with MCM; this implies that, even though the potential energy decreases in the annealing process, the Monte Carlo SA trajectory does not proceed towards the global minimum. Possible reasons for these differences between the two methods are discussed. It is concluded that, while SA presents attractive prospects for possibly improving or refining given structures, it must be considered inferior to MCM, at least in problems where little or no structural information is available for the molecule of interest.