Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review

Asmus O. Dohn*

*Corresponding author for this work

Research output: Contribution to journalReviewResearchpeer-review

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Abstract

The main concepts and important technical details of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) simulations are explained and illustrated with the intent of assisting newcomers in performing and gauging the accuracy of such simulations, focused on smaller molecules in solution. Beginners are advised on how to increase the reliability and accuracy of the simulations through benchmarking. Central considerations on methodologies for QM/MM Molecular Dynamics (MD) simulations are presented, alongside technical fundamentals regarding the construction and manipulation of simulation systems using the python-based Atomic Simulation Environment (ASE). A worked example of QM/MM Born–Oppenheimer MD is included, and a flowchart summarizing the most salient decisions and tasks within the methodology is presented.
Original languageEnglish
JournalInternational Journal of Quantum Chemistry
Volume120
Issue number21
Number of pages22
ISSN0020-7608
DOIs
Publication statusPublished - 2020

Keywords

  • Benchmarking
  • Electrostatic embedding
  • Implementation
  • QM/MM, QM/MM BOMD
  • Solvation
  • Structure

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