Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 μs/day using implicit solvent models.
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机译：分子动力学（MD）模拟现在在理论化学，生物学，物理学和材料科学的许多领域中发挥着关键作用。在许多情况下，此类计算受到执行感兴趣的计算所需的大量计算机时间的明显限制。在这里，我们提出了长时间步分子动力学（LTMD），这是一种显着加快MD模拟速度的方法。特别是，我们讨论了在LTMD中计算所需项的新方法以及与GPU实现密切相关的问题。在OpenMM MD库中实现的结果代码可以实现6倍的显着速度提高，从而使用隐式溶剂模型可以实现5 s /天的MD仿真。
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