Premium
Multi‐Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues
Author(s) -
Meier Katharina,
Choutko Alexandra,
Dolenc Jozica,
Eichenberger Andreas P.,
Riniker Sereina,
van Gunsteren Wilfred F.
Publication year - 2013
Publication title -
angewandte chemie international edition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.831
H-Index - 550
eISSN - 1521-3773
pISSN - 1433-7851
DOI - 10.1002/anie.201205408
Subject(s) - degrees of freedom (physics and chemistry) , resolution (logic) , process (computing) , statistical physics , computer science , boltzmann constant , molecular dynamics , physics , chemistry , computational chemistry , quantum mechanics , artificial intelligence , operating system
Abstract Theoretical‐computational modeling with an eye to explaining experimental observations in regard to a particular chemical phenomenon or process requires choices concerning essential degrees of freedom and types of interactions and the generation of a Boltzmann ensemble or trajectories of configurations. Depending on the degrees of freedom that are essential to the process of interest, for example, electronic or nuclear versus atomic, molecular or supra‐molecular, quantum‐ or classical‐mechanical equations of motion are to be used. In multi‐resolution simulation, various levels of resolution, for example, electronic, atomic, supra‐atomic or supra‐molecular, are combined in one model. This allows an enhancement of the computational efficiency, while maintaining sufficient detail with respect to particular degrees of freedom. The basic challenges and choices with respect to multi‐resolution modeling are reviewed and as an illustration the differential catalytic properties of two enzymes with similar folds but different substrates with respect to these substrates are explored using multi‐resolution simulation at the electronic, atomic and supra‐molecular levels of resolution.