Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan48824-1322, United States.
Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan48824-1322, United States.
J Chem Inf Model. 2023 Feb 13;63(3):711-717. doi: 10.1021/acs.jcim.2c01505. Epub 2023 Jan 31.
We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware.
我们已经在 AMD GPU 上移植和优化了 GPU 加速的 QUICK 和基于 AMBER 的量子力学/分子力学（QM/MM）实现。这包括 QUICK 中的整个 Fock 矩阵构建和力计算，包括单电子积分、双电子排斥积分、交换相关求积和线性代数运算。还介绍了 QUICK GPU 代码的一般性能改进。在 NVIDIA V100 和 AMD MI100 卡上进行的基准测试显示，对于 QUICK 的独立 HF/DFT 计算和 QUICK/AMBER 的 QM/MM 分子动力学模拟，两种硬件的性能相似。此外，与 QUICK/AMBER 21 版本相比，QM/MM 分子动力学模拟的速度显著提高。这大大增加了可以在最先进的计算机硬件上使用开源 QM/MM 软件解决的科学问题的范围。
