San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.
J Chem Inf Model. 2021 May 24;61(5):2109-2115. doi: 10.1021/acs.jcim.1c00169. Epub 2021 Apr 29.
The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API). Since QUICK is an open-source GPU-accelerated code with multi-GPU parallelization, users can take advantage of "free of charge" GPU-acceleration in their QM/MM simulations. In this work, we discuss implementation details and give usage examples. We also investigate energy conservation in typical QM/MM simulations performed at the microcanonical ensemble. Finally, benchmark results for two representative systems in bulk water, the -methylacetamide (NMA) molecule and the photoactive yellow protein (PYP), show the performance of QM/MM simulations with QUICK and AMBER using a varying number of CPU cores and GPUs. Our results highlight the acceleration obtained from a single or multiple GPUs; we observed speedups of up to 53× between a single GPU vs a single CPU core and of up to 2.6× when comparing four GPUs to a single GPU. Results also reveal speedups of up to 3.5× when the API is used instead of FBI.
量子力学/分子力学（QM/MM）方法是计算化学中一种必不可少且成熟的工具，已在文献中广泛应用于无数生物分子问题。在本出版物中，我们报告了将 QUantum Interaction Computational Kernel（QUICK）程序集成到 AMBER 中的 QM/MM 模拟中进行电子结构计算的方法。该集成可以通过文件接口（FBI）或应用程序编程接口（API）来实现。由于 QUICK 是一个带有 GPU 加速和多 GPU 并行化的开源代码，用户可以在 QM/MM 模拟中利用“免费”的 GPU 加速。在这项工作中，我们讨论了实现细节并给出了使用示例。我们还研究了在微正则系综中进行的典型 QM/MM 模拟中的能量守恒。最后，对两个代表体系（均处于体相水中）的基准测试结果，即 -甲基乙酰胺（NMA）分子和光活性黄色蛋白（PYP），展示了使用 QUICK 和 AMBER 进行 QM/MM 模拟的性能，涉及使用不同数量的 CPU 核和 GPU。我们的结果强调了单个或多个 GPU 获得的加速；我们观察到，与单个 CPU 核相比，单个 GPU 的加速比最高可达 53×，与单个 GPU 相比，四个 GPU 的加速比最高可达 2.6×。当使用 API 而不是 FBI 时，还可以获得高达 3.5×的加速。
