Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski’s Equality
Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski’s Equality
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通过 Metadynamics、Umbrella Sampling 和 Jarzynski 等式对固体/水界面吸附自由能计算进行方法评估
DOI：
10.1002/cphc.201701241
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发表时间：
2018
期刊：
影响因子：
2.9
通讯作者：
Yang Xiaoning
中科院分区：
文献类型：
--
作者：
Wei Qichao;Zhao Weilong;Yang Yang;Cui Beiliang;Xu Zhijun;Yang Xiaoning
在表征蛋白质/肽表面相互作用的相当大的兴趣，促使广泛的计算吸附自由能的计算研究。然而，在许多情况下，每个单独的研究都集中在自由能计算的应用到一个特定的系统，因此，很难联合收割机的结果到一个整体的画面选择一个适当的战略系统的利益。本文系统地比较和评价了三种成熟的计算算法，用于计算小分子在两种代表性表面上的吸附自由能。结果清楚地表明，所研究的界面系统的特性对吸附自由能计算的准确性和效率具有至关重要的影响。对于疏水表面，转向分子动力学表现出最高的效率，这似乎是一个有利的选择方法，用于增强采样模拟。然而，对于带电表面，只有伞形取样法有能力准确地探索吸附自由能表面。水层对表面的亲和力显著影响自由能计算方法的性能，特别是在靠近表面的区域。因此，提出了一个一般原则，如何区分方法和抽样问题的基础上调查系统的界面特性。
Considerable interest in characterizing protein/peptide–surface interactions has prompted extensive computational studies on calculations of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calculations to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well‐established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small molecules on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calculations. For the hydrophobic surface, steered molecular dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calculation methods, especially at the region close to the surface. Therefore, a general principle of how to discriminate between methodological and sampling issues based on the interfacial characteristics of the system under investigation is proposed.