Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys

被引:104
作者
Fu, Haohao [1 ]
Zhang, Hong [1 ]
Chen, Haochuan [1 ]
Shao, Xueguang [1 ,2 ,3 ]
Chipot, Christophe [4 ,5 ,6 ,7 ]
Cai, Wensheng [1 ,2 ]
机构
[1] Nankai Univ, Tianjin Key Lab Biosensing & Mol Recognit, Res Ctr Analyt Sci, Coll Chem, Tianjin 300071, Peoples R China
[2] Collaborat Innovat Ctr Chem Sci & Engn Tianjin, Tianjin 300071, Peoples R China
[3] State Key Lab Med Chem Biol, Tianjin 300071, Peoples R China
[4] CNRS, Lab Int Associe, F-54506 Vandoeuvre Les Nancy, France
[5] Univ Illinois, F-54506 Vandoeuvre Les Nancy, France
[6] Univ Lorraine, CNRS, UMR 7019, LPCT, F-54500 Vandoeuvre Les Nancy, France
[7] Univ Illinois, Dept Phys, 1110 West Green St, Urbana, IL 61801 USA
来源
JOURNAL OF PHYSICAL CHEMISTRY LETTERS | 2018年 / 9卷 / 16期
基金
中国国家自然科学基金;
关键词
ADAPTIVE BIASING FORCE; MOLECULAR-DYNAMICS SIMULATIONS; ENHANCED SAMPLING TECHNIQUES; BIOLOGICAL-SYSTEMS; ORTHOGONAL SPACE; MONTE-CARLO; RECONSTRUCTION; METADYNAMICS; ALGORITHMS; EFFICIENT;
D O I
10.1021/acs.jpclett.8b01994
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
A robust importance-sampling algorithm for mapping free-energy surfaces over geometrical variables, coined meta-eABF, is introduced. This algorithm shaves the free-energy barriers and floods valleys by incorporating a history-dependent potential term in the extended adaptive biasing force (eABF) framework. Numerical applications on both toy models and nontrivial examples indicate that meta-eABF explores the free energy surface significantly faster than either eABF or metadynamics (MtD) alone, without the need to stratify the reaction pathway. In some favorable cases, meta-eABF can be as much as five times faster than other importance-sampling algorithms. Many of the shortcomings inherent to eABF and MtD, like kinetic trapping in regions of configurational space already adequately sampled, the requirement of prior knowledge of the free-energy landscape to set up the simulation, are readily eliminated in meta-eABF. Meta-eABF, therefore, represents an appealing solution for a broad range of applications, especially when both eABF and MtD fail to achieve the desired result.
引用
收藏
页码:4738 / 4745
页数:15
相关论文
共 43 条
  • [1] Adaptively biased molecular dynamics for free energy calculations
    Babin, Volodymyr
    Roland, Christopher
    Sagui, Celeste
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (13)
  • [2] Metadynamics
    Barducci, Alessandro
    Bonomi, Massimiliano
    Parrinello, Michele
    [J]. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2011, 1 (05) : 826 - 843
  • [3] Well-tempered metadynamics: A smoothly converging and tunable free-energy method
    Barducci, Alessandro
    Bussi, Giovanni
    Parrinello, Michele
    [J]. PHYSICAL REVIEW LETTERS, 2008, 100 (02)
  • [4] Enhanced sampling techniques in molecular dynamics simulations of biological systems
    Bernardi, Rafael C.
    Melo, Marcelo C. R.
    Schulten, Klaus
    [J]. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 2015, 1850 (05): : 872 - 877
  • [5] ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines
    Chen, Haochuan
    Fu, Haohao
    Shao, Xueguang
    Chipot, Christophe
    Cai, Wensheng
    [J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2018, 58 (07) : 1315 - 1318
  • [6] Heating and flooding: A unified approach for rapid generation of free energy surfaces
    Chen, Ming
    Cuendet, Michel A.
    Tuckerman, Mark E.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2012, 137 (02)
  • [7] Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study
    Chipot, C
    Pohorille, A
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (01) : 281 - 290
  • [8] Frontiers in free-energy calculations of biological systems
    Chipot, Christophe
    [J]. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2014, 4 (01) : 71 - 89
  • [9] Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
    Comer, Jeffrey
    Phillips, James C.
    Schulten, Klaus
    Chipot, Christophe
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (12) : 5276 - 5285
  • [10] The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
    Comer, Jeffrey
    Gumbart, James C.
    Henin, Jerome
    Lelievre, Tony
    Pohorille, Andrew
    Chipot, Christophe
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2015, 119 (03) : 1129 - 1151