论文标题
部分可观测时空混沌系统的无模型预测
An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators
论文作者
论文摘要
杂交量子力学 /分子力学（QM / mm）模型成功地描述了生物大分子的特性。但是，大多数QM/MM方法都被限制在不切实际的气相模型上，从而限制了它们的适用性。在文献中，几项作品试图在周期性边界条件（PBC）中定义QM/MM模型，但是这些模型通常太耗时了，无法将一般适用于解决方案中的生物系统。在这里，我们在PBC中定义了一个简单有效的静电嵌入QM/MM模型，结合了静电电位拟合（ESPF）原子电荷的好处和粒子网 - 埃瓦尔德总和，可以有效地以合理的计算成本处理任意大小的系统。为了说明这一点，我们采用我们的方案来从拟南芥thaliana Cryctrome 1的模型中提取最低的单线激发能，其中包含大约93000原子，从而准确地重现了实验吸收最大值。
Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their applicability. In the literature, several works have attempted to define a QM/MM model in periodic boundary conditions (PBC) but frequently the models are too time-consuming for general applicability to biological systems in solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC combining the benefits of electrostatic potential fitted (ESPF) atomic charges and particle-mesh Ewald sums, that can efficiently treat systems of arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for arabidopsis thaliana cryptochrome 1 containing circa 93000 atoms, reproducing accurately the experimental absorption maximum.
