MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations
Fuente:
arXiv
Gespeichert in:
| Hauptverfasser: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Preprint |
| Veröffentlicht: |
2024
|
| Schlagworte: | |
| Online-Zugang: | |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| _version_ | 1866917787179417600 |
|---|---|
| author | Antalík, Andrej Levy, Andrea Kvedaravičiūtė, Sonata Johnson, Sophia K. Carrasco-Busturia, David Raghavan, Bharath Mouvet, François Acocella, Angela Das, Sambit Gavini, Vikram Mandelli, Davide Ippoliti, Emiliano Meloni, Simone Carloni, Paolo Rothlisberger, Ursula Olsen, Jógvan Magnus Haugaard |
| author_facet | Antalík, Andrej Levy, Andrea Kvedaravičiūtė, Sonata Johnson, Sophia K. Carrasco-Busturia, David Raghavan, Bharath Mouvet, François Acocella, Angela Das, Sambit Gavini, Vikram Mandelli, Davide Ippoliti, Emiliano Meloni, Simone Carloni, Paolo Rothlisberger, Ursula Olsen, Jógvan Magnus Haugaard |
| contents | 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 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_19035 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations Antalík, Andrej Levy, Andrea Kvedaravičiūtė, Sonata Johnson, Sophia K. Carrasco-Busturia, David Raghavan, Bharath Mouvet, François Acocella, Angela Das, Sambit Gavini, Vikram Mandelli, Davide Ippoliti, Emiliano Meloni, Simone Carloni, Paolo Rothlisberger, Ursula Olsen, Jógvan Magnus Haugaard Chemical Physics 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 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. |
| title | MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2403.19035 |