Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA...

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Bibliographic Details
Published in:Chemical science (Cambridge) 2019-08, Vol.1 (3), p.72-7211
Main Authors: Loco, Daniele, Lagardère, Louis, Cisneros, Gérardo A, Scalmani, Giovanni, Frisch, Michael, Lipparini, Filippo, Mennucci, Benedetta, Piquemal, Jean-Philip
Format: Article
Language:English
Subjects:
Amoeba
Chemical Sciences
Complex systems
Density functional theory
Dipoles
Embedded systems
Embedding
Energy conservation
Molecular dynamics
or physical chemistry
Pseudopotentials
Quantum mechanics
Subsystems
Theoretical and
Time dependence
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Summary:In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born-Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization. Hybrid DFT(Gaussian)/AMOEBA(Tinker/Tinker-HP) polarizable molecular dynamics including the QM/MM mutual polarization on large complex systems. Example of the thiazole orange dye buried in a DNA double helix, embedded in a sphere of water (16 500 atoms).
ISSN:2041-6520
2041-6539
DOI:10.1039/c9sc01745c