2020
DOI: 10.1021/acs.jctc.9b01152
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Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding

Abstract: With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper we present a systematic complexity reduction methodology which can br… Show more

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Cited by 26 publications
(37 citation statements)
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“…∆E linear = E linear − E cubic and ∆E fragment = E fragment − E linear . One such tool we have developed in this spirit is a complexity reduction framework [86,87] which takes large scale calculations, and uses them to decompose systems into coarse grained fragments. This fragment generation procedure is based on two metrics:…”
Section: B Complexity Reductionmentioning
confidence: 99%
“…∆E linear = E linear − E cubic and ∆E fragment = E fragment − E linear . One such tool we have developed in this spirit is a complexity reduction framework [86,87] which takes large scale calculations, and uses them to decompose systems into coarse grained fragments. This fragment generation procedure is based on two metrics:…”
Section: B Complexity Reductionmentioning
confidence: 99%
“…In our earlier publications [2], [23], we described a Complexity Reduction framework which uses the electronic density computed by QM calculations to reproduce the properties of a full system from calculations on only a subset of the system. The key ingredient of this analysis is the Fragment Bond Order, which is a generalization of atomic bond order to interactions between two arbitrary sets of atoms.…”
Section: Afb1 Afg2 Afb1mentioning
confidence: 99%
“…An interesting feature of that approach is its ability to decompose a molecular system into fragments from which one may compute a map summarizing the microscopic local interactions occurring within a molecular complex. 8,9 In the present study, we combine such a QM approach with a simulation stage based on a multi-scale polarizable Molecular Modeling, MM, one 10,11 to investigate the Potential Energy Surface, PES, of M pro /inhibitor complexes from Molecular Dynamics, MD, simulations in the aqueous phase.…”
Section: Despite Being Heavily Computationally Demanding Quantum Chementioning
confidence: 99%