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Open AccessArticle

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA
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Author to whom correspondence should be addressed.
Molecules 2018, 23(9), 2170; https://doi.org/10.3390/molecules23092170
Received: 24 July 2018 / Revised: 23 August 2018 / Accepted: 24 August 2018 / Published: 28 August 2018
In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system. View Full-Text
Keywords: combined QM/MM; molecular dynamics simulations; energy conservation; radial distribution function; adaptive partitioning combined QM/MM; molecular dynamics simulations; energy conservation; radial distribution function; adaptive partitioning
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MDPI and ACS Style

Duster, A.W.; Wang, C.-H.; Lin, H. Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes. Molecules 2018, 23, 2170.

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