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Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics

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Quantum Modeling of Complex Molecular Systems

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 21))

Abstract

Molecular dynamics simulations based on adaptive QM/MM methods feature on-the-fly reclassifications of atoms and molecular groups as either QM or MM without causing abrupt changes in the trajectory propagations, thus allowing QM subsystems to automatically change over time. Such treatments are not possible in the framework of conventional QM/MM, where the QM and MM partitions are predetermined and immutable throughout the simulation. The present contribution reviews the recent progress in the adaptive QM/MM algorithms developed by ourselves and our collaborators, namely the family of adaptive-partitioning (AP) schemes. Initially developed for the studies of solvated ions and molecules, AP methods have been extended to model large molecules, such as biopolymers, to monitor the exchange of solvent molecules between a protein active site and the bulk solvent, and to describe proton hopping in water via the Grotthuss mechanism.

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Abbreviations

AP:

Adaptive-partitioning

BEST:

Boundary-based-on-exchange-symmetry-theory

BZ:

Buffer zone

CG:

Coarse-grained

DAS:

Difference-based adaptive solvation

EEMB:

Electrostatically embedded many-body expansion

FIRES:

Flexible inner region ensemble separator

MD:

Molecular dynamics

MM:

Molecular-mechanics

mPAP:

Modified permuted adaptive-partitioning

NVE :

Microcanonical ensemble

NVT :

Canonical ensemble

ONIOM-XS:

Our own n-layered integrated molecular orbital and molecular mechanics-exchange of solvent

QM:

Quantum-mechanics

QM/MM:

Combined quantum-mechanics/molecular mechanics

QM/MM-LPS:

Combined quantum-mechanics/molecular mechanics with large primary-subsystem

PAP:

Permuted adaptive-partitioning

PS:

Primary subsystem

RC:

Redistributed charge

RCD:

Redistributed charge and dipole

SAP:

Sorted adaptive-partitioning

SCMP:

Size-consistent multi-partitioning

SS:

Secondary subsystem

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Acknowledgments

This work is supported by National Science Foundation (CHE-0952337). This work used the Extreme Science and Engineering Discovery Environment (XSEDE) under grant CHE-140070, which is supported by National Science Foundation grant number ACI-1053575. HL thanks the Camille & Henry Dreyfus Foundation for support (TH-14-028). We are grateful to Adam Duster for critically reading our manuscript.

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The authors declare no competing financial interest.

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  1. Department of Chemistry, University of Colorado Denver, Denver, CO, 80217-3364, USA

    Soroosh Pezeshki & Hai Lin

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  1. Soroosh Pezeshki
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Editors and Affiliations

  1. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Jean-Louis Rivail

  2. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Manuel Ruiz-Lopez

  3. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Xavier Assfeld

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Pezeshki, S., Lin, H. (2015). Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics. In: Rivail, JL., Ruiz-Lopez, M., Assfeld, X. (eds) Quantum Modeling of Complex Molecular Systems. Challenges and Advances in Computational Chemistry and Physics, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-319-21626-3_3

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