Literature DB >> 18647014

A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations.

Lianqing Zheng1, Irina O Carbone, Alexey Lugovskoy, Bernd A Berg, Wei Yang.   

Abstract

Recently, we developed an efficient free energy simulation technique, the simulated scaling (SS) method [H. Li et al., J. Chem. Phys. 126, 024106 (2007)], in the framework of generalized ensemble simulations. In the SS simulations, random walks in the scaling parameter space are realized so that both phase space overlap sampling and conformational space sampling can be simultaneously enhanced. To flatten the distribution in the scaling parameter space, in the original SS implementation, the Wang-Landau recursion was employed due to its well-known recursion capability. In the Wang-Landau recursion based SS free energy simulation scheme, at the early stage, recursion efficiencies are high and free energy regions are quickly located, although at this stage, the errors of estimated free energy values are large; at the later stage, the errors of estimated free energy values become smaller, however, recursions become increasingly slow and free energy refinements require very long simulation time. In order to robustly resolve this efficiency problem during free energy refinements, a hybrid recursion strategy is presented in this paper. Specifically, we let the Wang-Landau update method take care of the early stage recursion: the location of target free energy regions, and let the adaptive reweighting method take care of the late stage recursion: the refinements of free energy values. As comparably studied in the model systems, among three possible recursion procedures, the adaptive reweighting recursion approach is the least favorable one because of its low recursion efficiency during free energy region locations; and compared to the original Wang-Landau recursion approach, the proposed hybrid recursion technique can be more robust to guarantee free energy simulation efficiencies.

Mesh:

Year:  2008        PMID: 18647014     DOI: 10.1063/1.2953321

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

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Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2011-11-28       Impact factor: 3.488

2.  Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2009-05-21       Impact factor: 3.488

3.  Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems.

Authors:  Lianqing Zheng; Mengen Chen; Wei Yang
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-15       Impact factor: 11.205

4.  Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

Authors:  Ilja V Khavrutskii; Anders Wallqvist
Journal:  J Chem Theory Comput       Date:  2010-11-09       Impact factor: 6.006

  4 in total

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