Schwörer Magnus, Lorenzen Konstantin, Mathias Gerald, Tavan Paul
Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany.
J Chem Phys. 2015 Mar 14;142(10):104108. doi: 10.1063/1.4914329.
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.
最近,有人提出了一种用于混合量子力学/分子力学(QM/MM)分子动力学(MD)模拟的新方法[施沃勒等人,《化学物理杂志》138, 244103 (2013)]。在此方法中,作用于原子的力通过基于网格的密度泛函理论(DFT)计算溶质分子的力,以及通过可极化分子力学(PMM)力场计算由几个10³ - 10⁵个分子组成的大溶剂环境的力,作为DFT/PMM混合哈密顿量的负梯度。静电相互作用通过分层快速多极子方法(FMM)有效描述。采用这种FMM技术的最新进展[洛伦岑等人,《化学理论与计算杂志》10, 3244 (2014)],其特别意味着计算量与系统大小严格呈线性缩放,并将这种改进的FMM方法应用于模拟系统的DFT和PMM片段之间相互作用的计算,在此,我们展示了如何进一步提高此类DFT/PMM - MD模拟的效率和准确性。以效率增益和准确性增益的乘积衡量,对于嵌入水中(PMM)的丙氨酸二肽(DFT),总性能的提升约为一个数量级。我们还证明,计算的DFT和PMM - MD部分的联合并行实现能够高效利用高性能计算系统。相关软件可在线获取。