Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

Yang, Y. Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang

doi:10.1063/1.4943004

Title: Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

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Abstract

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Authors:

Yang, Y. Isaac ^[1]; Zhang, Jun; Che, Xing; Yang, Lijiang

Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China)

Publication Date:: Mon Mar 07 00:00:00 EST 2016

OSTI Identifier:: 22660874

Resource Type:: Journal Article

Journal Name:: Journal of Chemical Physics

Additional Journal Information:: Journal Volume: 144; Journal Issue: 9; Other Information: (c) 2016 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9606

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; DYNAMICS; EFFICIENCY; FREE ENERGY; MOLECULAR DYNAMICS METHOD; POTENTIAL ENERGY; SAMPLING; SIMULATION

Citation Formats


                    Yang, Y. Isaac, Zhang, Jun, Che, Xing, Yang, Lijiang, Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.  United States: N. p., 2016. 
        Web.  doi:10.1063/1.4943004.

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                    Yang, Y. Isaac, Zhang, Jun, Che, Xing, Yang, Lijiang, Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn, & Biodynamic Optical Imaging Center, Peking University, Beijing 100871. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.  United States.  https://doi.org/10.1063/1.4943004

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                    Yang, Y. Isaac, Zhang, Jun, Che, Xing, Yang, Lijiang, Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871. 2016.  
        "Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling".  United States.  https://doi.org/10.1063/1.4943004.

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@article{osti_22660874,

  title        = {Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling},

  author       = {Yang, Y. Isaac and Zhang, Jun and Che, Xing and Yang, Lijiang and Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn and Biodynamic Optical Imaging Center, Peking University, Beijing 100871},

  abstractNote = {In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.},

  doi          = {10.1063/1.4943004},

  url          = {https://www.osti.gov/biblio/22660874},
  journal      = {Journal of Chemical Physics},

  issn         = {0021-9606},

  number       = 9,

  volume       = 144,

  place        = {United States},

  year         = {Mon Mar 07 00:00:00 EST 2016},

  month        = {Mon Mar 07 00:00:00 EST 2016}

}

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