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Progress in Chemistry 2018, Vol. 30 Issue (7): 921-931 DOI: 10.7536/PC171026 Previous Articles   Next Articles

Special Issue: 计算化学

• Review •

Importance Sampling Methods and Free Energy Calculations

Haochuan Chen1, Haohao Fu1, Xueguang Shao1,2, Wensheng Cai1*   

  1. 1. Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Collaborative Innovation Center of Chemical Science and Engineering(Tianjin), Nankai University, Tianjin 300071, China;
    2. State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
  • Received: Revised: Online: Published:
  • Supported by:
    The work was supported by the National Natural Science Foundation of China(No. 21373117, 21773125).
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Molecular dynamics(MD) simulations with free energy calculations have been widely applied to chemistry, biology and material science. However, within the timescale of conventional MD simulations, ergodic sampling in phase space is limited due to high free-energy barriers. Insufficient sampling may, in turn, lead to poor convergence of the free energy calculations based on conventional MD simulations. Enhanced sampling is a powerful technique to overcome this difficulty, among which importance sampling method is the most representative one. In this paper, the principles and progress of four prevalent importance sampling methods, namely, umbrella sampling(US), metadynamics(MtD), adaptive biasing force(ABF) and temperature accelerated molecular dynamics(TAMD), are described and reviewed. In particular, the recent developments of ABF, such as the extended ABF(eABF) considered as the second generation of ABF, and the extended generalized ABF(egABF) methods designed for high dimensional sampling, are comprehensively summarized. The advantages and disadvantages of US, MtD, TAMD and ABF with their variants are presented and compared. Furthermore, challenges and outlooks for free energy calculation with importance sampling methods are discussed and prospected. Specifically, possible further improvements to current ABF methods, such as combination with accelerated molecular dynamics(aMD) simulations or string methods to enhance sampling efficiency in high-dimensional spaces are put forward.
Contents
1 Introduction
2 Umbrella sampling
3 Metadynamics
4 Adaptive biasing force
4.1 Extended adaptive biasing force
4.2 Extended generalized adaptive biasing force
5 Temperature accelerated molecular dynamics
6 Conclusion and outlook
Key words: molecular dynamics simulation, free energy calculation, importance sampling, umbrella sampling, metadynamics, adaptive biasing force, temperature accelerated molecular dynamics

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