The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry.
The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry.
复制标题
用于旋转对称周期性边界条件的扩展八壳法。
DOI：
10.1002/jcc.26545
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发表时间：
2021
影响因子：
3
通讯作者：
Brooks,BernardR
中科院分区：
文献类型：
--
作者：
Prasad,Samarjeet;Simmonett,AndrewC;Meana-Pañeda,Rubén;Brooks,BernardR
分子动力学模拟并行化的第八壳层方法此前已被证明是在大过程计数时效率最优的方法。然而，在目前的公式中，周期边界条件(PBC)只支持P1空间群，因此不支持反射和/或旋转晶体对称性。在这项工作中，我们概述了扩展的第八壳(EES)方法的发展和实现，该方法通过使用与ES方法相比的扩展的输入区域来实现旋转对称。它只模拟非对称单位，并用对应于P21 PBC的图像来传递坐标和力。P21PBC在脂质双层模拟中有应用，因为它可以用来允许脂质交换小叶，从而快速平衡两层之间的化学势差。我们的结果表明，EES方法在大量的过程中都是有效的，并且可以用来模拟具有P21对称性的正交晶体。
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 theP1 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 toP21PBC. TheP21PBC 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 withP21symmetry in an orthorhombic crystal.