Monte Carlo/energy minimization

Combined Monte Carlo/Energy Minimization Methods... 

Global Minimum in Docking Simulations A Monte Carlo Energy Minimization Approach Using Bezier Splines. 

Trosset, J. Y. Scheraga, H. A. (1998). Reaching the global minimum in docking simulations a Monte Carlo energy minimization approach using Bezier splines. Proc Natl Acad Sci U S A 95(14), 8011-5. 

W. C. Guida, R. S. Bohacek, and M. D. Erion,/. Comput. Chem., 13,214 (1992). Probing the Conformational Space Available to Inhibitors in the Thermolysin Active Site Using Monte Carlo/Energy Minimization Techniques. 

Molecular dynamics (MD), Monte Carlo, energy minimization, and related algorithms are used for refining macromolecular structures, using data from x-ray crystallography and NMR. MD can also be employed to simulate macromolecular motions over timescales ranging from femtoseconds to nanoseconds (1). 

Toulouse and Umrigar have recently developed a Monte Carlo energy minimization scheme that allows minimization of Cl, orbital, and Jastrow parameters. The method is based on a linear expansion of the normalized wave function (f>(x p) in terms of the parameters p = ... 

A Monte Carlo/energy minimization (MC/EM) conformational search for the enamine intermediate derivatives revealed conformations where one face of the... 

A. Nayeem, J. Vila, and H. A. Scheraga. A comparative study of the simulated-annealing and monte carlo-with-minimization approaches to the minimum-energy structures of polypeptides [met]-enkephalin. J. Comp. Chem., 12(5) 594-605, 1991. 

Minimization of the Monte Carlo energy estimate minimizes the sum of the true value and the error due to the finite sample. Although the variational principle provides a lower bound for the energy, there is no lower bound for the error of an energy estimate. Fixed sample energy minimization is therefore notoriously unstable [140, 146], Optimization algorithms based on Newton s, linear and perturbative methods have been proposed [43,48, 140,147-151]. 

The first step in studying phenomenological theories (Ginzburg-Landau theories and membrane theories) has usually been to minimize the free energy functional of the model. Fluctuations are then included at a later stage, e.g., using Monte Carlo simulations. The latter will be discussed in Sec. V and Chapter 14. 

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