Key Laboratory for Mechanics in Fluid Solid Coupling Systems, Institute of Mechanics, Chinese Academy of Sciences, No.15, Beisihuan West Road, Haidian District, Beijing, 100190, People's Republic of China.
School of Engineering Science, University of Chinese Academy of Sciences, No.19(A), Yuquan Road, Shijingshan District, Beijing, 100049, China.
J Mol Model. 2021 Jan 28;27(2):55. doi: 10.1007/s00894-020-04661-5.
Evaluation of effective coarse graining (CG) degree and reasonable speedup relative to all-atomistic (AA) model was conducted to provide a basis for building appropriate larger-scale model. The reproducibility of atomistic conformation and temperature transferability both act as the analysis criteria to resolve the maximum acceptable CG degree. Taking short- and long time spans into account simultaneously in the estimation of computational speedup, a dynamic scaling factor is accessible in fitting mean squared displacement ratio of CG to AA as an exponential function. Computing loss in parallel running is an indispensable component in acceleration, which was also added in the evaluation. Subsequently, a quantified prediction of CG speedup arises as a multiplication of dynamic scaling factor, computing loss, time step, and the square of reduction in the number of degrees of freedom. Polyethylene oxide was adopted as a reference system to execute the direct Boltzmann inversion and iterative Boltzmann inversion. Bonded and non-bonded potentials were calculated in CG models with 1~4 monomers per bead. The effective CG degree was determined as two at the most with a speedup of four orders magnitude over AA in this study. Determination of effectiveness CG degree and the corresponding speedup prediction provide available tools in larger spatiotemporal-scale calculations.
为了构建合适的更大规模模型，对有效粗粒化（CG）程度和相对于全原子（AA）模型的合理加速进行了评估。原子构象的再现性和温度传递性都是解决最大可接受 CG 程度的分析标准。在估计计算加速时，同时考虑短时间跨度和长时间跨度，可通过拟合 CG 与 AA 的均方位移比的指数函数获得动态缩放因子。并行运行中的计算损失是加速的不可或缺的组成部分，在评估中也进行了添加。随后，CG 加速的量化预测作为动态缩放因子、计算损失、时间步长和自由度减少平方的乘积出现。聚环氧乙烷被用作参考系统来执行直接玻尔兹曼反演和迭代玻尔兹曼反演。在 CG 模型中，每个珠子使用 1 到 4 个单体计算键合和非键合势。在这项研究中，有效 CG 程度最多确定为两个，相对于 AA 的加速达到了四个数量级。确定有效 CG 程度和相应的加速预测为更大时空尺度计算提供了可用的工具。
