NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
J Chem Phys. 2011 Mar 28;134(12):124115. doi: 10.1063/1.3568010.
The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the energy gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting gradients are compared with numerical gradients for the test molecular systems: (H(2)O)(64), alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO self-consistent charge calculation. It is also shown that the energy gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational costs. The fully analytic FMO gradient is parallelized with an efficiency of about 98% on 32 nodes.
Z- 向量方程被推导和实现，用于求解由于外部静电势引起的响应项，并且在分块分子轨道（FMO）方法的框架中，将相应的贡献添加到能量梯度中。为了在蛋白质等大型分子的实际求解中，利用 FMO 方法中碎片的局部性质，通过建立自洽 Z-向量方法对这些方程进行解耦。将所得梯度与测试分子系统的数值梯度进行比较：（H2O）（64）、丙氨酸十聚体、与 PDB ID 为 1UAO 的水合 chignolin 以及 Trp-cage 小蛋白结构（PDB ID：1L2Y）。计算响应贡献的计算时间与 FMO 自洽电荷计算的时间相当或更短。还表明，静电二聚体近似的能量梯度是完全解析的，这显著降低了计算成本。完全解析的 FMO 梯度在 32 个节点上并行化效率约为 98%。
