Caliber based spectral gap optimization of order parameters (SGOOP) for sampling complex molecular systems
| Autor: | Tiwary, Pratyush, Berne, B. J. |
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| Rok vydání: | 2015 |
| Předmět: | |
| Druh dokumentu: | Working Paper |
| DOI: | 10.1073/pnas.1600917113 |
| Popis: | In modern day simulations of many-body systems much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CV) or reaction coordinates. A vast array of enhanced sampling methods are based on the identification and biasing of these low-dimensional order parameters, whose fluctuations are important in driving rare events of interest. Here describe a new algorithm for finding optimal low-dimensional collective variables for use in enhanced sampling biasing methods like umbrella sampling, metadynamics and related methods, when limited prior static and dynamic information is known about the system, and a much larger set of candidate CVs is specified. The algorithm involves estimating the best combination of these candidate CVs, as quantified by a maximum path entropy estimate of the spectral gap for dynamics viewed as a function of that CV. Through multiple practical examples, we show how this post-processing procedure can lead to optimization of CV and several orders of magnitude improvement in the convergence of the free energy calculated through metadynamics, essentially giving the ability to extract useful information even from unsuccessful metadynamics runs. Comment: 7 pages, 4 figures; corrected missing figure number and added a reference |
| Databáze: | arXiv |
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