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Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review
Author(s) -
Dohn Asmus O.
Publication year - 2020
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.26343
Subject(s) - python (programming language) , molecular dynamics , computer science , embedding , benchmarking , statistical physics , flowchart , computational science , computational chemistry , physics , chemistry , artificial intelligence , marketing , business , programming language , operating system
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.