Document Detail


Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.
MedLine Citation:
PMID:  23795244     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation.
Authors:
Mahmoud Moradi; Emad Tajkhorshid
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-5-17
Journal Detail:
Title:  The journal of physical chemistry letters     Volume:  4     ISSN:  1948-7185     ISO Abbreviation:  J Phys Chem Lett     Publication Date:  2013 Jun 
Date Detail:
Created Date:  2013-6-24     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101526034     Medline TA:  J Phys Chem Lett     Country:  -    
Other Details:
Languages:  ENG     Pagination:  1882-1887     Citation Subset:  -    
Affiliation:
Center for Biophysics and Computational Biology, Department of Biochemistry, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
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