SHAKE is a widely used algorithm to impose general holonomic constraints during molecular simulations. By imposing constraints on stiff degrees of freedom that require integration with small time steps (without the constraints) we are able to calculate trajectories with time steps larger by approximately a factor of two. The larger time step makes it possible to run longer simulations. Another approach to extend the scope of Molecular Dynamics is parallelization. Parallelization speeds up the calculation of the forces between the atoms and makes it possible to compute longer trajectories with better statistics for thermodynamic and kinetic averages. A combination of SHAKE and parallelism is therefore highly desired. Unfortunately, the most widely used SHAKE algorithm (of bond relaxation) is inappropriate for parallelization and alternatives are needed. The alternatives must minimize communication, lead to good load balancing, and offer significantly better performance than the bond relaxation approach. The algorithm should also scale with the number of processors. We describe the theory behind different implementations of constrained dynamics on parallel systems, and their implementation on common architectures.

中文翻译：

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SHAKE并行化。

SHAKE 是一种广泛使用的算法，用于在分子模拟期间施加一般完整约束。通过对需要以小时间步长（无约束）进行积分的刚性自由度施加约束，我们能够计算出时间步长大约为 2 倍的轨迹。更大的时间步长使得运行更长的模拟成为可能。另一种扩展分子动力学范围的方法是并行化。并行化加速了原子之间力的计算，并可以计算更长的轨迹，并具有更好的热力学和动力学平均值统计数据。因此，非常需要 SHAKE 和并行性的组合。很遗憾，最广泛使用的 SHAKE 算法（键松弛）不适用于并行化，需要替代方案。替代方案必须最大限度地减少通信，实现良好的负载平衡，并提供比绑定松弛方法明显更好的性能。该算法还应该随着处理器的数量而扩展。我们描述了并行系统上约束动态的不同实现背后的理论，以及它们在通用架构上的实现。