Huang Lulu, Massa Lou
Center for Computational Materials Science, Naval Research Laboratory, Washington, DC 20375-5341.
Theochem. 2010 Dec;962(1-3):72-79. doi: 10.1016/j.theochem.2010.09.017.
The Kernel Energy Method (KEM) provides a way to calculate the ab-initio energy of very large biological molecules. The results are accurate, and the computational time reduced. However, by use of a list of double kernel interactions a significant additional reduction of computational effort may be achieved, still retaining ab-initio accuracy. A numerical comparison of the indices that name the known double interactions in question, allow one to list higher order interactions having the property of topological continuity within the full molecule of interest. When, that list of interactions is unpacked, as a kernel expansion, which weights the relative importance of each kernel in an expression for the total molecular energy, high accuracy, and a further significant reduction in computational effort results. A KEM molecular energy calculation based upon the HF/STO3G chemical model, is applied to the protein insulin, as an illustration.
核能量方法（KEM）提供了一种计算非常大的生物分子的从头算能量的方法。结果准确，计算时间减少。然而，通过使用双核相互作用列表，可以显著进一步减少计算量，同时仍保持从头算精度。对命名相关已知双相互作用的指标进行数值比较，能够列出在整个感兴趣的分子内具有拓扑连续性的高阶相互作用。当将该相互作用列表作为核展开进行拆解时，它会在总分子能量表达式中权衡每个核的相对重要性，从而实现高精度并进一步显著减少计算量。作为示例，基于HF/STO3G化学模型的KEM分子能量计算被应用于蛋白质胰岛素。
