Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 15, Issue 6, Pages 3810-3823Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.9b00093
Keywords
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Funding
- Danish Council for Independent Research (DFF) through the Sapere Aude research career program [DFF-1325-00091, DFF-1323-00744]
- Carlsberg Foundation [CF15-0823]
- Research Council of Norway through its Centres of Excellence scheme [262695]
- European Union's Horizon 2020 program from project HPC-LEAP (MSCA-ITN-2014-EJD) [642069]
- European Union's Horizon 2020 program from the BioExcel Center of Excellence (EINFRA-5-2015) [675728]
- Deutsche Forschungsgemeinschaft [FOR 2518]
- Swiss National Science Foundation via the NCCR MUST
- DeIC National HPC Centre at the University of Southern Denmark, the Norwegian Supercomputing Program (NOTUR) [NN4654K]
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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.
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