Renison C Alicia, Fernandes Kyle D, Naidoo Kevin J
Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
J Comput Chem. 2015 Jul 5;36(18):1410-9. doi: 10.1002/jcc.23938. Epub 2015 May 14.
This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.
本文描述了量子增压库（QSL）的扩展，用于执行量子力学（QM）梯度和优化计算以及混合量子力学与分子力学（QM/MM）分子动力学模拟。在上述计算/模拟中，继双电子积分之后，积分导数是计算成本最高的部分。本文提出了在图形处理单元（GPU）上加速单电子和双电子积分导数计算的算法。结果表明，与运行使用高效施莱格尔方法处理s轨道和l轨道的优化串行版本GAMESS-UK的单个中央处理器相比，在单个GPU上进行哈特里-福克从头算梯度计算的速度快达9.3倍。使用6-31G基组，在真空和39 Å水球中（分别有45个QM原子和24843个点电荷）对纤维二糖进行了基准QM和QM/MM分子动力学模拟。在单个GPU上，QSL可以在全双精度下执行每天9.7皮秒的从头算QM动力学和每天6.4皮秒的QM/MM动力学。© 2015威利期刊公司。
