Laboratory of Computational Biology, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
J Comput Chem. 2021 Jul 15;42(19):1373-1383. doi: 10.1002/jcc.26545. Epub 2021 May 11.
The Eighth-Shell method for parallelization of molecular dynamics simulations has previously been shown to be the most optimal for efficiency at large process counts. However, in its current formulation only the P1 space group is supported for periodic boundary conditions (PBC) and thus reflection and/or rotational crystal symmetries are not supported. In this work, we outline the development and implementation of the Extended Eighth-Shell (EES) method that allows rotational symmetry by using an extended import region compared to the ES method. It simulates only the asymmetric unit and communicates coordinates and forces with images that correspond to P2 PBC. The P2 PBC has application in lipid bilayer simulations as it can be used to allow lipids to switch leaftlets, thus rapidly balancing the chemical potential difference between the two layers. Our results show that the EES method scales efficiently over large number of processes and can be used for simulations with P2 symmetry in an orthorhombic crystal.
第八壳层方法已被证明是在大规模进程计数下效率最高的分子动力学模拟并行化方法。然而，在其当前的形式中，仅支持 P1 空间群用于周期性边界条件（PBC），因此不支持反射和/或旋转晶体对称性。在这项工作中，我们概述了扩展第八壳层（EES）方法的开发和实现，该方法通过与 ES 方法相比使用扩展的导入区域来允许旋转对称性。它仅模拟不对称单元，并与对应于 P2 PBC 的图像进行坐标和力的通信。P2 PBC 在脂质双层模拟中具有应用，因为它可以用于允许脂质切换叶瓣，从而快速平衡两层之间的化学势差。我们的结果表明，EES 方法在大量进程上能够高效扩展，并且可以用于具有正交晶体 P2 对称性的模拟。
