3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.
3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.
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DOI：
10.1021/ct200815v
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发表时间：
2012-06
影响因子：
5.5
通讯作者：
V. Sergiievskyi;M. Fedorov
中科院分区：
文献类型：
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作者：
V. Sergiievskyi;M. Fedorov
在本文中，我们提出了一种快速准确的方法来模拟水中有机分子的溶剂化特性，主要关注于预测小有机化合物的溶剂化（水合）自由能。该方法基于（i）分子理论、三维参考相互作用位点模型（3DRISM）的组合； (ii) 用于求解高维 3DRISM 积分方程的快速多重网格算法； (iii) 最近引入了通过适当缩放的分子部分体积对 3DRISM 溶剂化自由能进行通用校正 (UC)（3DRISM-UC, Palmer 等人, J. Phys.: Condens. Matter2010, 22, 492101）。快速多重网格算法是该方法的核心，因为它有助于降低与求解 3DRISM 方程相关的高计算成本。为了便于该方法的未来应用，我们对一组几种模型溶质进行了算法基准测试，以找到最佳网格参数并测试算法的性能和准确性。我们已经证明，所提出的新多重网格算法平均比简单的 Picard 方法快 24 倍，比 3DRISM 社区当前积极使用的 MDIIS 方法至少快 3.5 倍（例如，MDIIS 方法最近已在最近发布的 AmberTools 1.4 分子建模包中的新 3DRISM 隐式溶剂例程中实现（Luchko 等人 J. Chem. Theory Comput. 2010，然后，我们在一组 99 种有机化合物上对多重网格算法进行了基准测试，结果表明，在标准个人计算机上，每个小有机分子（10-20 个原子）所需的平均计算时间为 3.5 分钟。我们还根据相应的实验数据对该组中所有化合物的预测溶剂化自由能值进行了基准测试。利用3DRISM-UC模型，小分子有机化合物水溶液的溶剂化自由能的计算结果与实验结果之间可以获得良好的相关性（相关系数0.97，均方根偏差<1 kcal/mol）。
In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarking of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good correlation between calculated and experimental results for solvation free energies of aqueous solutions of small organic compounds (correlation coefficient 0.97, root-mean-square deviation <1 kcal/mol).