MiMiC: A high-performance framework for multiscale molecular dynamics simulations

The Journal of Chemical Physics, vol. 161

Abstract

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

Authors 16

1. Andrej Antalík

   École Polytechnique Fédérale de Lausanne

   Affiliation as printed

   Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne 1 , CH-1015 Lausanne, Switzerland

2. Andrea Levy

   École Polytechnique Fédérale de Lausanne

   Affiliation as printed

   Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne 1 , CH-1015 Lausanne, Switzerland

3. Sonata Kvedaravičiūtė

   Technical University of Denmark

   Affiliation as printed

   DTU Chemistry, Technical University of Denmark (DTU) 2 , DK-2800 Kongens Lyngby, Denmark

4. Sophia K. Johnson

   École Polytechnique Fédérale de Lausanne

   Affiliation as printed

   Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne 1 , CH-1015 Lausanne, Switzerland

5. David Carrasco‐Busturia

   Technical University of Denmark

   Affiliation as printed

   DTU Chemistry, Technical University of Denmark (DTU) 2 , DK-2800 Kongens Lyngby, Denmark

6. Bharath Raghavan Aachen Department of Physics

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH 3 , Jülich 52428, Germany

   Department of Physics, RWTH Aachen University 4 , Aachen 52074, Germany

7. François Mouvet

   École Polytechnique Fédérale de Lausanne

   Affiliation as printed

   Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne 1 , CH-1015 Lausanne, Switzerland

8. Angela Acocella

   Cineca

   Affiliation as printed

   CINECA 5 , 40033 Casalecchio di Reno, BO, Italy

9. Sambit Kumar Das

   University of Michigan

   Affiliation as printed

   Department of Mechanical Engineering, University of Michigan 6 , Ann Arbor, Michigan 48109, USA

10. Vikram Gavini

    University of Michigan

    Affiliation as printed

    Department of Materials Science and Engineering, University of Michigan 7 , Ann Arbor, Michigan 48109, USA

    Department of Mechanical Engineering, University of Michigan 6 , Ann Arbor, Michigan 48109, USA

11. Davide Mandelli

    Forschungszentrum Jülich

    Affiliation as printed

    Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH 3 , Jülich 52428, Germany

12. Emiliano Ippoliti

    Forschungszentrum Jülich

    Affiliation as printed

    Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH 3 , Jülich 52428, Germany

13. Simone Meloni

    University of Ferrara

    Affiliation as printed

    Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie (DOCPAS), Università degli Studi di Ferrara (Unife) 8 , I-44121 Ferrara, Italy

14. Paolo Carloni Aachen Department of Physics

    Forschungszentrum Jülich · RWTH Aachen University

    Affiliation as printed

    Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH 3 , Jülich 52428, Germany

    Department of Physics, RWTH Aachen University 4 , Aachen 52074, Germany

15. Ursula Röthlisberger

    École Polytechnique Fédérale de Lausanne

    Affiliation as printed

    Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne 1 , CH-1015 Lausanne, Switzerland

16. Jógvan Magnus Haugaard Olsen

    Technical University of Denmark

    Affiliation as printed

    DTU Chemistry, Technical University of Denmark (DTU) 2 , DK-2800 Kongens Lyngby, Denmark