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A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations
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10.1063/1.2953321
/content/aip/journal/jcp/129/3/10.1063/1.2953321
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/3/10.1063/1.2953321
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

The setup of model system 1: The alchemical transformation between the amino acids asparagine (ASN) and leucine (LEU) in gas phase. The portion of leucine is colored in black and the portion of asparagine is colored in gray.

Image of FIG. 2.
FIG. 2.

The setup of model system 2: Glutamine (GLN) 27 of antibody 5c8 is mutated to glutamic acid (GLU) 27 when 5c8 binds antigen cd40L. (a) The alchemical transformation between the amino acids glutamic acid and glutamine; the portion of glutamine is colored in blue and the portion of glutamic acid is colored in red. (b) The GSBP setup on the complex between antibody 5c8 and antigen cd40L. Glutamine 27 (colored based on the atom type) of antibody 5c8 is treated as the center of the water (colored in red) sphere. The protein portion is colored in blue.

Image of FIG. 3.
FIG. 3.

(a) The time evolutions of the averages of estimated free energy differences in model study 1 based on various recursion methods. (b) The time evolutions of the standard deviations of 100 independent replicas in model system 1 based on various recursion methods: The original Wang–Landau recursion (SS), the remedy version of Wang–Landau recursion (SS 1.01 and SS 1.001), and the hybrid recursion (HSS 1.01 and HSS 1.001). (c) The time evolutions of the values in F-tests for the comparisons of the SS 1.01 curve vs the HSS 1.01 curve and the SS 1.001 curve versus the HSS 1.001 curve.

Image of FIG. 4.
FIG. 4.

(a) The time evolutions of the averages of estimated free energy differences in model study based on the hybrid recursion method and the adaptive reweighting method. (b) The time evolutions of the standard deviations of ten independent replicas in model study 2 based on the hybrid recursion method and the adaptive reweighting method.

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/content/aip/journal/jcp/129/3/10.1063/1.2953321
2008-07-18
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/3/10.1063/1.2953321
10.1063/1.2953321
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