Second derivatives in generalized born theory
Second derivatives in generalized born theory
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DOI：
10.1002/jcc.20479
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发表时间：
2006-11-15
影响因子：
3
通讯作者：
Case, David A.
中科院分区：
文献类型：
--
作者：
Brown, Russell A.;Case, David A.
广义玻恩溶剂化模型提供了一种流行的方法，包括静电方面的溶剂化自由能的分析模型，只依赖于原子坐标，电荷和介电半径。在这里，我们描述了如何相对于笛卡尔坐标的二阶导数可以计算在一个有效的方式，可以分布在多个处理器。这种方法使得各种新的方法分析这些隐式溶剂化模型。我们在这里说明了三个这些方法：使用牛顿-拉夫森优化，以获得精确的最小值的解决方案;正常模式分析计算溶剂化对DNA的机械性能的影响;和MM/GBSA模型中的构型熵的计算。这些想法的实现，使用琥珀广义玻恩模型，可在核酸构建器（NAB）代码中使用，我们给出了具有多达45，000个原子的蛋白质的例子。该代码已经实现了并行计算机使用的OpenMP和MPI环境，以及良好的并行扩展被视为多达144个OpenMP处理线程或NIPI处理任务。(C)2006 Wiley Periodicals，Inc.
Generalized Born solvation models offer a popular method of including electrostatic aspects of solvation free energies within an analytical model that depends only upon atomic coordinates, charges, and dielectric radii. Here, we describe how second derivatives with respect to Cartesian coordinates can be computed in an efficient manner that can be distributed over multiple processors. This approach makes possible a variety of new methods of analysis for these implicit solvation models. We illustrate three of these methods here: the use of Newton-Raphson optimization to obtain precise minima in solution; normal mode analysis to compute solvation effects on the mechanical properties of DNA; and the calculation of configurational entropies in the MM/GBSA model. An implementation of these ideas, using the Amber generalized Born model, is available in the nucleic acid builder (NAB) code, and we present examples for proteins with up to 45,000 atoms. The code has been implemented for parallel computers using both the OpenMP and MPI environments, and good parallel scaling is seen with as many as 144 OpenMP processing threads or NIPI processing tasks. (C) 2006 Wiley Periodicals, Inc.