Adaptive partitioning molecular dynamics using an extended Hamiltonian approach

2021 ◽  
Vol 155 (14) ◽  
pp. 144104
Author(s):  
Jim Bachmann ◽  
Nikos L. Doltsinis
Keyword(s):  
Molecular Dynamics ◽  
Hamiltonian Approach ◽  
Adaptive Partitioning

Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel

2019 ◽  
Vol 15 (2) ◽  
pp. 892-905 ◽  
Author(s):  
Adam W. Duster ◽  
Christina M. Garza ◽  
Baris O. Aydintug ◽  
Mikias B. Negussie ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Proton Transport ◽  
Adaptive Partitioning ◽  
Dynamics Simulations

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

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2170 ◽  
Author(s):  
Adam Duster ◽  
Chun-Hung Wang ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Model System ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
Adaptive Partitioning ◽  
Pap Method ◽  
Dynamics Simulations

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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