Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
J Chem Theory Comput. 2008 Oct 14;4(10):1600-9. doi: 10.1021/ct800193a.
We report the implementation of the generalized solvent boundary potential (GSBP) [ Im , W. , Bernèche , S. , and Roux , B. J. Chem. Phys. 2001, 114, 2924 ] in the framework of semiempirical hybrid quantum mechanical/molecular mechanical (QM/MM) methods. Application of the GSBP is connected with a significant overhead that is dominated by numerical solutions of the Poisson-Boltzmann equation for continuous charge distributions. Three approaches are presented that accelerate computation of the values at the boundary of the simulation box and in the interior of the macromolecule and solvent. It is shown that these methods reduce the computational overhead of the GSBP significantly with only minimal loss of accuracy. The accuracy of the GSBP to represent long-range electrostatic interactions is assessed for an extensive set of its inherent parameters, and a set of optimal parameters is defined. On this basis, the overhead and the savings of the GSBP are quantified for model systems of different sizes in the range of 7000 to 40 000 atoms. We find that the savings compensate for the overhead in systems larger than 12 500 atoms. Beyond this system size, the GSBP reduces the computational cost significantly, by 70% and more for large systems (>25 000 atoms).
我们在半经验混合量子力学/分子力学（QM/MM）方法的框架内实现了广义溶剂边界势（GSBP）[Im, W., Bernèche, S., and Roux, B. J. Chem. Phys. 2001, 114, 2924]。GSBP 的应用与显著的开销有关，这主要由连续电荷分布的泊松-玻尔兹曼方程的数值解决定。本文提出了三种方法来加速模拟盒边界和大分子和溶剂内部的数值计算。结果表明，这些方法在不降低精度的情况下，显著降低了 GSBP 的计算开销。我们评估了 GSBP 代表长程静电相互作用的准确性，为其广泛的固有参数定义了一组最佳参数。在此基础上，我们对不同大小的模型系统（范围从 7000 到 40000 个原子）量化了 GSBP 的开销和节省。我们发现，对于大于 12500 个原子的系统，节省可以弥补开销。超出这个系统规模，GSBP 会显著降低计算成本，对于大型系统（>25000 个原子），计算成本可降低 70%甚至更多。
