Making PLUMED Fly: A Tutorial on Optimizing Performance

doi:10.1021/acs.jpcb.5c07562

2026-02-24

Daniele Rapetti

Massimiliano Bonomi *

Carlo Camilloni *

Giovanni Bussi *

Gareth A. Tribello *

DOI：10.1021/acs.jpcb.5c07562

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摘要

En 中文

PLUMED是一个开源软件包，广泛应用于分析并增强分子动力学模拟，该软件可与大多数现有的分子动力学软件协同工作。虽然PLUMED计算的计算成本通常与分子动力学代码的力评估相比可忽略不计，但该软件正越来越多地被用于确定更耗计算资源的复杂描述符。对于这些应用，性能优化变得至关重要。在本教程中，我们介绍了一个近期实现的工具，可用于可靠地测量代码性能。随后，我们使用该工具生成详细的性能基准，展示了如何通过使用基于向量的命令而非单个标量操作来优化大量距离、角度或扭转角计算。接着，我们展示了基准测试结果，说明了如何优化原子有序参数和二级结构变量的计算。在整个教程及我们的实现中，我们致力于解释用于优化计算的各种算法技巧。我们希望这能让其他人理解这些方法并在自己的计算中应用它们。

Keyword:

Chemical calculations

Computer simulations

Molecular dynamics

Software

Thermodynamic properties

期刊

The Journal of Physical Chemistry B

IF:

2.9

论文数:

767

被引数:

机构

sissa

学者数:

论文数: 49

被引数: 2

Institut Pasteur and Université Paris Cité and CNRS

学者数:

论文数: 9

被引数: 0

queen's university belfast

学者数:

1.0K

论文数: 510

被引数: 0

university of milano

学者数:

219

论文数: 120

被引数: 0

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