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

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https://hdl.handle.net/10037/16193
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article.pdf (2.674Mb)
Accepted manuscript version (PDF)
Dato
2019-09-09
Type
Journal article
Tidsskriftartikkel
Peer reviewed

Forfatter
Bolnykh, Viacheslav; Olsen, Jógvan Magnus Haugaard; Meloni, Simone; Bircher, Martin Peter; Ippoliti, Emiliano; Carloni, Paolo; Rothlisberger, Ursula
Sammendrag
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.
Beskrivelse
Accepted manuscript version. Published version in Journal of Chemical Theory and Computation available at https://doi.org/10.1021/acs.jctc.9b00424.
Forlag
American Chemical Society
Sitering
Bolnykh, V., Olsen, J.M.H., Meloni, S., Bircher, M.P., Ippoliti, E., Carloni, P. & Rothlisberger, U. (2019). Extreme Scalability of DFT-based QM/MM MD Simulations Using MiMiC. Journal of Chemical Theory and Computation. https://doi.org/10.1021/acs.jctc.9b00424
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