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Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

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submitted on 02.05.2019 and posted on 03.05.2019 by Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher, Emiliano Ippoliti, Paolo Carloni, Ursula Rothlisberger
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 GGA and hybrid 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 of 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.

Funding

High Performance Computing in Life Sciences, Engineering And Physics

European Commission

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Danish Council for Independent Research (DFF) through the Sapere Aude research career program (Grant ID: 1325-00091 and 1323-00744)

Carlsberg Foundation (Grant ID: CF15-0823)

Hylleraas Center

The Research Council of Norway

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Centre of Excellence for Biomolecular Research

European Commission

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Molecular Ultrafast Science and Technology (MUST)

Swiss National Science Foundation

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FOR 2518:  Functional dynamics of ion channels and transporters - DynIon -

Deutsche Forschungsgemeinschaft

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History

Email Address of Submitting Author

v.bolnykh@fz-juelich.de

Institution

RWTH Aachen / The Cyprus Institute / Forschungszentrum Juelich

Country

Germany

ORCID For Submitting Author

0000-0002-7090-1993

Declaration of Conflict of Interest

No conflict of interest

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in Journal of Chemical Theory and Computation

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