期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 15, 期 10, 页码 5601-5613出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.9b00424
关键词
-
资金
- European Union [642069, 675728]
- Danish Council for Independent Research (DFF) through the Sapere Aude research career program [DFF-1325-00091, DFF-1323-00744]
- Carlsberg Foundation [CF15-0823]
- Research Council of Norway through its Centres of Excellence scheme [262695]
- Deutsche Forschungsgemeinschaft [FOR 2518]
- Swiss National Science Foundation via the NCCR MUST
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing non-hybrid and hybrid GGA exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据