Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.
Hiroaki NishizawaYoshifumi NishimuraMasato KobayashiStephan IrleHiromi NakaiPublished in: Journal of computational chemistry (2016)
The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc.
Keyphrases
- molecular dynamics
- dendritic cells
- molecular dynamics simulations
- quality improvement
- density functional theory
- deep learning
- high efficiency
- blood brain barrier
- machine learning
- monte carlo
- immune response
- molecular docking
- dna binding
- mass spectrometry
- early stage
- single molecule
- high resolution
- molecularly imprinted
- electron transfer