Document Detail


Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk.
MedLine Citation:
PMID:  19466826     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the lambda space, with lambda being any thermodynamic variable that characterizes a canonical ensemble such as the reciprocal temperature beta or any variable that the Hamiltonian depends on. The partition function is determined by minimizing the difference of the thermal conjugates of lambda (the energy in the case of lambda = beta), defined as the difference between the value from the dynamically updated derivatives of the partition function and the value directly measured from simulation. Higher-order derivatives of the partition function are included to enhance the Brownian motion in the lambda space. The method is much less sensitive to the system size, and to the size of lambda window than other methods. On the two dimensional Ising model, it is shown that the method asymptotically converges the partition function, and the error of the logarithm of the partition function is much smaller than the algorithm using the Wang-Landau recursive scheme. The method is also applied to off-lattice model proteins, the AB models, in which cases many low energy states are found in different models.
Authors:
Cheng Zhang; Jianpeng Ma
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  130     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2009 May 
Date Detail:
Created Date:  2009-05-26     Completed Date:  2009-07-28     Revised Date:  2014-09-16    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  194112     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Computer Simulation*
Models, Molecular
Motion*
Protein Folding
Proteins / chemistry
Stochastic Processes
Temperature*
Thermodynamics
Grant Support
ID/Acronym/Agency:
R01 GM067801/GM/NIGMS NIH HHS; R01 GM067801-06A1/GM/NIGMS NIH HHS; R01 GM067801-07/GM/NIGMS NIH HHS; R01-GM067801/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Proteins
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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