Large-scale DFT calculations in implicit solventA case study on the T4 lysozyme L99A/M102Q protein
Large-scale DFT calculations in implicit solventA case study on the T4 lysozyme L99A/M102Q protein
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DOI：
10.1002/qua.24075
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发表时间：
2013-03-15
影响因子：
2.2
通讯作者：
Skylaris, Chris-Kriton
中科院分区：
文献类型：
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作者：
Dziedzic, Jacek;Fox, Stephen J.;Skylaris, Chris-Kriton
最近，基于真实的空间中的非齐次泊松方程的直接解的第一原理电子结构计算的隐式溶剂化模型的变体已经被开发。这些隐式溶剂化模型是非常优雅的，从物理的角度来看，作为溶质腔是直接定义通过电子密度的等值面，和分子电荷极化自洽周围的溶质的介电连续体的反应场。然而，这些模型的实施在技术上是复杂的，需要非常小心。这类模型的用户需要一定程度的谨慎，因为需要为一些数值参数提供适当的值，以获得最准确和物理相关的结果。在这里，我们描述了这些数值参数各自涉及溶剂模型的哪些部分，并使用已在ONETEP程序中实现的溶剂化模型详细研究了它们如何影响计算，用于线性标度密度泛函理论（DFT）计算。由于ONETEP能够进行数千个原子的DFT计算，我们将重点放在整个2602原子T4溶菌酶L99/M102 Q蛋白质的proteinligand复合物的案例研究的数值参数的调查。我们研究对溶剂化能和结合能的影响，这是计算药物优化和其他类型的生物分子模拟的关键量。我们提出了这些参数的最佳选择适合于常规生产计算。(c)2012 Wiley Periodicals，Inc.
Recently, variants of implicit solvation models for first principles electronic structure calculations based on a direct solution of the nonhomogeneous Poisson equation in real space have been developed. These implicit solvation models are very elegant from a physical point of view as the solute cavity is defined directly via isosurfaces of the electronic density, and the molecular charge is polarized self-consistently by the reaction field of the dielectric continuum which surrounds the solute. Nevertheless, the implementation of these models is technically complex and requires great care. A certain level of care is required from users of such models as a number of numerical parameters need to be given appropriate values to obtain the most accurate and physically relevant results. Here, we describe in what parts of the solvent model each of these numerical parameters is involved and present a detailed study of how they can affect the calculation, using the solvation model which has been implemented in the ONETEP program for linear-scaling density functional theory (DFT) calculations. As ONETEP is capable of DFT calculations with thousands of atoms, we focus our investigation of the numerical parameters with a case study on proteinligand complexes of the entire 2602-atom T4 Lysozyme L99/M102Q protein. We examine effects on solvation energies and binding energies, which are critical quantities for computational drug optimization and other types of biomolecular simulations. We propose optimal choices of these parameters suitable for routine production calculations. (c) 2012 Wiley Periodicals, Inc.