An-hui Wang, Zhi-chao Zhang, Guo-hui Li. Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules[J]. Chinese Journal of Chemical Physics , 2019, 32(3): 277-286. doi: 10.1063/1674-0068/cjcp1905091
Citation: An-hui Wang, Zhi-chao Zhang, Guo-hui Li. Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules[J]. Chinese Journal of Chemical Physics , 2019, 32(3): 277-286. doi: 10.1063/1674-0068/cjcp1905091

Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules

doi: 10.1063/1674-0068/cjcp1905091
Funds:  This work was supported by the National Natural Science Foundation of China (No.31700647, No.21625302, and No.21573217).
  • Received Date: 2019-05-10
  • Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions. However, when applied to complex biological macromolecules, the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes, leading to inherent timescale gaps between molecular dynamics simulations and real biological processes. To address this issue, several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics. In this review, the theoretical basis, practical applications, and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized. Furthermore, the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.
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Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules

doi: 10.1063/1674-0068/cjcp1905091
Funds:  This work was supported by the National Natural Science Foundation of China (No.31700647, No.21625302, and No.21573217).

Abstract: Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions. However, when applied to complex biological macromolecules, the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes, leading to inherent timescale gaps between molecular dynamics simulations and real biological processes. To address this issue, several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics. In this review, the theoretical basis, practical applications, and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized. Furthermore, the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.

An-hui Wang, Zhi-chao Zhang, Guo-hui Li. Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules[J]. Chinese Journal of Chemical Physics , 2019, 32(3): 277-286. doi: 10.1063/1674-0068/cjcp1905091
Citation: An-hui Wang, Zhi-chao Zhang, Guo-hui Li. Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules[J]. Chinese Journal of Chemical Physics , 2019, 32(3): 277-286. doi: 10.1063/1674-0068/cjcp1905091

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