Olsen Jógvan Magnus Haugaard, Bolnykh Viacheslav, Meloni Simone, Ippoliti Emiliano, Bircher Martin P, Carloni Paolo, Rothlisberger Ursula
Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , UiT The Arctic University of Norway , N-9037 Tromsø , Norway.
Department of Physics , RWTH Aachen University , 52056 Aachen , Germany.
J Chem Theory Comput. 2019 Jun 11;15(6):3810-3823. doi: 10.1021/acs.jctc.9b00093. Epub 2019 May 6.
We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the existing parallelization strategies used by the coupled programs while maintaining a high degree of flexibility. MiMiC has been used in a new electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) implementation coupling the highly efficient CPMD and GROMACS programs, but it can also be extended to use other programs. The framework can also be utilized to extend the partitioning of the system into several domains that can be treated using different models, such as models based on wave function or density functional theory as well as coarse-graining and continuum models. The new QM/MM implementation treats long-range electrostatic QM-MM interactions through the multipoles of the QM subsystem which substantially reduces the computational cost without loss of accuracy compared to an exact treatment. This enables QM/MM molecular dynamics (MD) simulations of very large systems.
我们提出了一种用于计算化学多尺度建模的灵活高效框架（MiMiC）。它基于具有松散耦合程序的多程序多数据（MPMD）模型。程序之间的快速数据交换通过使用MPI互通器来实现。这使得在保持高度灵活性的同时，能够利用耦合程序所使用的现有并行化策略。MiMiC已被用于一种新的静电嵌入量子力学/分子力学（QM/MM）实现中，该实现耦合了高效的CPMD和GROMACS程序，但它也可以扩展以使用其他程序。该框架还可用于将系统划分为多个可使用不同模型处理的域，例如基于波函数或密度泛函理论的模型以及粗粒化和连续介质模型。新的QM/MM实现通过QM子系统的多极来处理长程静电QM-MM相互作用，与精确处理相比，这在不损失精度的情况下大幅降低了计算成本。这使得能够对非常大的系统进行QM/MM分子动力学（MD）模拟。
