Sparse sampling of water density fluctuations near liquid-vapor coexistence
Sparse sampling of water density fluctuations near liquid-vapor coexistence
复制标题
液汽共存附近水密度波动的稀疏采样
DOI：
10.1080/08927022.2018.1457218
复制
发表时间：
2017
影响因子：
2.1
通讯作者：
Patel, Amish J.
中科院分区：
文献类型：
--
作者：
Xi, Erte;Marks, Sean M.;Fialoke, Suruchi;Patel, Amish J.
水密度涨落的自由能量学决定了疏水溶质的水化作用及其相互作用和组装。这种自由能量学的表征通常使用增强的采样技术，例如伞形采样。在伞形抽样中，从相邻有偏模拟获得的序参数分布必须重叠，以便估计有偏系综间的自由能差。通常需要许多有偏差的模拟来确保这种重叠，这会带来高昂的计算成本。我们最近引入了一种稀疏采样方法，该方法通过使用热力学积分来估计有偏差的系综之间的自由能差，从而绕过了重叠要求。在这里，我们建立在稀疏采样的基础上，并对其进行推广，以表征接近气液共存系统中水密度波动的自由能量学。我们还引入了合理的启发式方法来选择偏置势能参数和自适应精炼它们的策略，这有助于准确和有效地估计这种自由能级。我们通过描述散装水中大体积空化的自由能量来说明这一方法。我们还使用稀疏采样来表征受限于两个疏水平板之间的水的毛细蒸发的自由能。在这两种情况下，稀疏抽样都比伞形抽样快近两个数量级。考虑到它的效率，稀疏采样方法特别适合于表征伞状采样昂贵得令人望而却步的系统的自由能量环境。
The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterisation of such free energetics is typically performed using enhanced sampling techniques such as umbrella sampling. In umbrella sampling, order parameter distributions obtained from adjacent biased simulations must overlap in order to estimate free energy differences between biased ensembles. Many biased simulations are typically required to ensure such overlap, which exacts a steep computational cost. We recently introduced a sparse sampling method, which circumvents the overlap requirement by using thermodynamic integration to estimate free energy differences between biased ensembles. Here we build upon and generalise sparse sampling for characterising the free energetics of water density fluctuations in systems near liquid-vapor coexistence. We also introduce sensible heuristics for choosing the biasing potential parameters and strategies for adaptively refining them, which facilitate the estimation of such free energetics accurately and efficiently. We illustrate the method by characterising the free energetics of cavitation in a large volume in bulk water. We also use sparse sampling to characterise the free energetics of capillary evaporation for water confined between two hydrophobic plates. In both cases, sparse sampling is nearly two orders of magnitude faster than umbrella sampling. Given its efficiency, the sparse sampling method is particularly well suited for characterising free energy landscapes for systems wherein umbrella sampling is prohibitively expensive.
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DOI：
10.1063/1.3532939
发表时间：
2010-10
期刊：
The Journal of chemical physics
影响因子：
--
作者：
P. Varilly;Amish J. Patel;D. Chandler
通讯作者：
P. Varilly;Amish J. Patel;D. Chandler
DOI：
10.1021/jp909048f
发表时间：
2010-02-04
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Patel AJ;Varilly P;Chandler D
通讯作者：
Chandler D
影响因子：
4.4
作者：
Desgranges, Caroline;Delhommelle, Jerome
通讯作者：
Delhommelle, Jerome
影响因子：
15
作者：
Rotenberg, Benjamin;Patel, Amish J.;Chandler, David
通讯作者：
Chandler, David
影响因子：
4.4
作者：
Tan, Zhiqiang;Gallicchio, Emilio;Levy, Ronald M.
通讯作者：
Levy, Ronald M.