期刊
JOURNAL OF CHEMICAL INFORMATION AND MODELING
卷 60, 期 11, 页码 5366-5374出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.0c00279
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资金
- National Natural Science Foundation of China [21773125]
- China Postdoctoral Science Foundation [bs6619012]
- Natural Science Foundation of Tianjin, China [18JCYBJC20500]
- Agence National de la Recherche (ProteaseInAction)
- Centre National de la Recherche Scientifique (CNRS) through an integrated program of scientific cooperation (PICS) with China
An ad-hoc, yet widely adopted approach to investigate complex molecular objects in motion using importance-sampling schemes involves two steps, namely (i) mapping the multidimensional free-energy landscape that characterizes the movements in the molecular object at hand and (ii) finding the most probable transition path connecting basins of the free-energy hyperplane. To achieve this goal, we turn to an importance-sampling algorithm, coined well-tempered metadynamics-extended adaptive biasing force (WTM-eABF), aimed at mapping rugged free-energy landscapes, combined with a path-searching algorithm, which we call multidimensional lowest energy (MULE), to identify the underlying minimum free-energy pathway in the collective-variable space of interest. First, the well-tempered feature of the importance-sampling scheme confers to the latter an asymptotic convergence, while the overall algorithm inherits the advantage of high sampling efficiency of its predecessor, meta-eABF, making its performance less sensitive to user-defined parameters. Second, the Dijkstra algorithm implemented in MULE is able to identify with utmost efficiency a pathway that satisfies minimum free energy of activation among all the possible routes in the multidimensional free-energy landscape. Numerical simulations of three molecular assemblies indicate that association of WTM-eABF and MULE constitutes a reliable, efficient and robust approach for exploring coupled movements in complex molecular objects. On account of its ease of use and intrinsic performance, we expect WTM-eABF and MULE to become a tool of choice for both experts and nonexperts interested in the thermodynamics and the kinetics of processes relevant to chemistry and biology.
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