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 language | English |
|---|---|
| Article number | e26343 |
| Journal | International Journal of Quantum Chemistry |
| Volume | 120 |
| Issue number | 21 |
| DOIs | |
| Publication status | Published - 1 Nov 2020 |
Bibliographical note
Funding Information:Independent Research Fund Denmark, Grant/Award Number: 8021‐00347B; Icelandic Research Fund, Grant/Award Numbers: 174244‐051, 196279‐051 Funding information
Funding Information:
The author thanks G. Levi and E. Ö Jónsson for useful input. Funding was provided by the Icelandic Research Fund, grants 196279‐051 and 174244‐051, as well as from the Independent Research Fund Denmark under Grant no. 8021‐00347B.
Publisher Copyright:
© 2020 Wiley Periodicals LLC
Other keywords
- benchmarking
- electrostatic embedding
- implementation
- QM/MM
- QM/MM BOMD
- solvation
- structure