Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency
Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency
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DOI：
10.1039/c8sm00868j
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发表时间：
2018-09-21
期刊：
影响因子：
3.4
通讯作者：
Guenza, Marina G.
中科院分区：
文献类型：
--
作者：
Dinpajooh, Mohammadhasan;Guenza, Marina G.
积分方程粗粒化 (IECG) 方法是一种有前途的聚合物熔体高级粗粒化 (CG) 方法，具有从软球到多个 CG 位点的可变分辨率，从而保持了与相关原子模拟的结构和热力学一致性。与原子描述相比，粗粒化过程会导致自由能表面更平滑、电势范围更长、给定聚合物的相互作用位点数量减少等等。由于这些变化对 CG 模型的计算效率具有相互竞争的影响，因此在研究粗粒度对 CG 分子动力学模拟中计算加速的影响时需要小心。例如，处理长程 CG 相互作用需要选择截止距离，其中包括有效 CG 势和力的吸引部分。特别是，我们展示了有效 CG 势的范围和曲率的复杂性质、合适的 CG 时间步长的选择、截止距离的选择、分子动力学算法以及 CG 自由能表面的平滑度如何影响 IECG 模拟的效率。通过与相对短链聚合物熔体的原子模拟的直接比较，我们发现最高级别的CG（软球）的总体计算效率最高，对于各种CG级别/分辨率，计算效率的总体提高约为10（6）-10（8）。因此，IECG方法在聚合物体系的分子动力学模拟中具有重要的应用。最后，利用标准空间分解算法，提出了不同级别 CG 的 IECG 模拟的并行可扩展性。对于相当大量的处理器，可以观察到最佳的并行扩展。尽管本研究是使用 IECG 方法进行的，但其关于 CG 水平与计算效率之间关系的结果是通用的，适用于任何正确构建的 CG 模型。
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical consistencies with the related atomistic simulations. When compared to the atomistic description, the procedure of coarse-graining results in smoother free energy surfaces, longer-ranged potentials, a decrease in the number of interaction sites for a given polymer, and more. Because these changes have competing effects on the computational efficiency of the CG model, care needs to be taken when studying the effect of coarse-graining on the computational speed-up in CG molecular dynamics simulations. For instance, treatment of long-range CG interactions requires the selection of cutoff distances that include the attractive part of the effective CG potential and force. In particular, we show how the complex nature of the range and curvature of the effective CG potential, the selection of a suitable CG timestep, the choice of the cutoff distance, the molecular dynamics algorithms, and the smoothness of the CG free energy surface affect the efficiency of IECG simulations. By direct comparison with the atomistic simulations of relatively short chain polymer melts, we find that the overall computational efficiency is highest for the highest level of CG (soft spheres), with an overall improvement of the computational efficiency being about 10(6)-10(8) for various CG levels/resolutions. Therefore, the IECG method can have important applications in molecular dynamics simulations of polymeric systems. Finally, making use of the standard spatial decomposition algorithm, the parallel scalability of the IECG simulations for various levels of CG is presented. Optimal parallel scaling is observed for a reasonably large number of processors. Although this study is performed using the IECG approach, its results on the relation between the level of CG and the computational efficiency are general and apply to any properly-constructed CG model.