Reweighted ensemble dynamics simulations: Theory, improvement, and application

doi:10.1088/1674-1056/24/6/060202

中国物理B ›› 2015, Vol. 24 ›› Issue (6): 60202-060202.doi: 10.1088/1674-1056/24/6/060202

Reweighted ensemble dynamics simulations: Theory, improvement, and application

龚麟宸^a, 周昕^b, 欧阳钟灿^{a c}

a Center for Advanced Study, Tsinghua University, Beijing 100084, China;
b School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China;
c Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China

收稿日期:2014-11-20 修回日期:2015-01-19 出版日期:2015-06-05 发布日期:2015-06-05
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 11175250).

Reweighted ensemble dynamics simulations: Theory, improvement, and application

Gong Lin-Chen (龚麟宸)^a, Zhou Xin (周昕)^b, Ouyang Zhong-Can (欧阳钟灿)^{a c}

a Center for Advanced Study, Tsinghua University, Beijing 100084, China;
b School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China;
c Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China

Received:2014-11-20 Revised:2015-01-19 Online:2015-06-05 Published:2015-06-05
Contact: Zhou Xin E-mail:xzhou@ucas.ac.cn
About author:02.70.Ns; 87.15.A-; 82.20.Wt
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 11175250).

摘要/Abstract

摘要：

Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.

关键词: ensemble dynamics simulations, peptides, enhanced sampling, metastable states

Abstract:

Key words: ensemble dynamics simulations, peptides, enhanced sampling, metastable states

中图分类号: (Molecular dynamics and particle methods)

02.70.Ns

87.15.A- (Theory, modeling, and computer simulation) 82.20.Wt (Computational modeling; simulation)

龚麟宸, 周昕, 欧阳钟灿. Reweighted ensemble dynamics simulations: Theory, improvement, and application[J]. 中国物理B, 2015, 24(6): 60202-060202.

Gong Lin-Chen (龚麟宸), Zhou Xin (周昕), Ouyang Zhong-Can (欧阳钟灿). Reweighted ensemble dynamics simulations: Theory, improvement, and application[J]. Chin. Phys. B, 2015, 24(6): 60202-060202.

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Reweighted ensemble dynamics simulations: Theory, improvement, and application

Reweighted ensemble dynamics simulations: Theory, improvement, and application

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