STORMM:结构和拓学复制分子力学用于化学模拟
David S Cerutti1, Rafal Wiewiora1, Simon Boothroyd1
1Psivant Therapeutics, Boston, Massachusetts 02210, USA.
The Journal of chemical physics
|July 15, 2024
概括
结构和拓复制分子力学 (STORMM) 代码加速了GPU上的分子模拟,为药物发现应用提供了显著的性能提升. 这个开源引擎提高了分子动力学模拟的吞吐量和准确性.
科学领域:
- 计算化学是一种计算化学.
- 分子动力学模拟的模拟.
- 高性能计算的高性能计算.
背景情况:
- 分子模拟对于理解分子力学和药物发现至关重要.
- 现有的分子动力学引擎面临性能限制,特别是大数据集.
- 为像GPU这样的现代硬件优化模拟对于推进研究至关重要.
研究的目的:
- 引入结构和拓复制分子力学 (STORMM) 代码作为一个高性能分子模拟引擎.
- 为了实现快速的原型设计和开发新的原子模拟方法用于药物发现.
- 为了提高分子动力学模拟的吞吐量和可扩展性.
主要方法:
- 为GPU和向量化CPU优化下一代分子模拟引擎 (STORMM) 的开发.
- 实施新的技术来调整数值精度,数学运算和高吞吐量内存使用.
- 工程解决方案将内存密集型方面 (粒子网格映射,价值相互作用) 转化为计算问题.
- 利用可访问的类与详细的文档进行细粒度并行性和算法开发.
主要成果:
- STORMM实现了小分子和蛋白质分子动力学模拟常规代码的几十到几百倍的吞吐量.
- 与现有程序相比,工程范式显著提高了可扩展性.
- 新的数值方法在坐标压缩和查找表中提供了更高的精度.
结论:
- STORMM代表了分子模拟性能和可扩展性的重大进步.
- 开源代码有助于开发用于药物发现的先进计算工具.
- 发动机的设计非常适合在现代硬件上处理大规模的分子机械计算.
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