This title appears in the Scientific Report :
2019
Please use the identifier:
http://dx.doi.org/10.1021/acs.jctc.9b00093 in citations.
Please use the identifier: http://hdl.handle.net/2128/25089 in citations.
MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
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...
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Personal Name(s): | Olsen, Jógvan Magnus Haugaard (Corresponding author) |
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Bolnykh, Viacheslav / Meloni, Simone / Ippoliti, Emiliano / Bircher, Martin P. / Carloni, Paolo / Rothlisberger, Ursula | |
Contributing Institute: |
Computational Biomedicine; INM-9 Computational Biomedicine; IAS-5 |
Published in: | Journal of chemical theory and computation, 15 (2019) 6, S. 3810 - 3823 |
Imprint: |
Washington, DC
2019
|
DOI: |
10.1021/acs.jctc.9b00093 |
PubMed ID: |
30998344 |
Document Type: |
Journal Article |
Research Program: |
Theory, modelling and simulation |
Link: |
Restricted Restricted Published on 2019-04-18. Available in OpenAccess from 2020-04-18. Published on 2019-04-18. Available in OpenAccess from 2020-04-18. |
Publikationsportal JuSER |
Please use the identifier: http://hdl.handle.net/2128/25089 in citations.
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 wave function 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. |