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

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
A DusterHai Lin

Abstract

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.

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Citations

Apr 21, 2021·Physical Chemistry Chemical Physics : PCCP·Hiroshi C WatanabeYohichi Suzuki
Aug 10, 2021·Journal of Chemical Theory and Computation·Eleftherios LambrosFrancesco Paesani
Nov 21, 2020·Journal of Chemical Theory and Computation·Eleftherios LambrosFrancesco Paesani
Aug 10, 2021·Wiley Interdisciplinary Reviews. Computational Molecular Science·Jorge NochebuenaG Andrés Cisneros
Jan 16, 2019·Journal of Chemical Theory and Computation·Adam W DusterHai Lin
Sep 26, 2019·Journal of Chemical Theory and Computation·Adam W Duster, Hai Lin
May 17, 2019·Journal of Chemical Theory and Computation·Hiroshi C Watanabe, Qiang Cui
Jul 17, 2019·Journal of Chemical Theory and Computation·Boyi ZhangHenry F Schaefer
Feb 8, 2022·Journal of Chemical Theory and Computation·Xin ChenJiali Gao

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Software Mentioned

QMMM
PAP
mPAP
SAP
MNDO
Open
MP
NVE
HAMBC
NAMD

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