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MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

preprint
submitted on 26.01.2019 and posted on 28.01.2019 by Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger
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 wavefunction 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.

Funding

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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High Performance Computing in Life Sciences, Engineering And Physics

European Commission

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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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History

Email Address of Submitting Author

jogvan.m.olsen@uit.no

Institution

UiT The Arctic University of Norway

Country

Norway

ORCID For Submitting Author

0000-0001-7487-944X

Declaration of Conflict of Interest

No conflict of interest

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in Journal of Chemical Theory and Computation

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