Universal QM/MM approaches for general nanoscale applications
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …
chemical phenomena in complex molecular environments. Whereas this modeling approach …
From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …
fields, enables researchers to investigate biological systems at the molecular level with …
General many-body framework for data-driven potentials with arbitrary quantum mechanical accuracy: Water as a case study
We present a general framework for the development of data-driven many-body (MB)
potential energy functions (MB-QM PEFs) that represent the interactions between small …
potential energy functions (MB-QM PEFs) that represent the interactions between small …
QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations
H Lin, Y Zhang, S Pezeshki, AW Duster, B Wang… - Computer Physics …, 2024 - Elsevier
Combined quantum mechanical and molecular mechanical (QM/MM) methods play an
important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose …
important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose …
Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy …
TS Hofer, PH Hünenberger - The Journal of chemical physics, 2018 - pubs.aip.org
Absolute proton hydration free energy, surface potential of water, and redox potential of the
hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and …
hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and …
Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here?
Adaptive quantum‐mechanics/molecular‐mechanics (QM/MM) methods feature on‐the‐fly
reclassification of atoms as QM or MM during a molecular dynamics (MD) simulation …
reclassification of atoms as QM or MM during a molecular dynamics (MD) simulation …
[HTML][HTML] Molecular systems with open boundaries: Theory and simulation
L Delle Site, M Praprotnik - Physics Reports, 2017 - Elsevier
Typical experimental setups for molecular systems must deal with a certain coupling to the
external environment, that is, the system is open and exchanges mass, momentum, and …
external environment, that is, the system is open and exchanges mass, momentum, and …
[HTML][HTML] Data-driven many-body potentials from density functional theory for aqueous phase chemistry
Density functional theory (DFT) has been applied to modeling molecular interactions in
water for over three decades. The ubiquity of water in chemical and biological processes …
water for over three decades. The ubiquity of water in chemical and biological processes …
From adaptive resolution to molecular dynamics of open systems
We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on
discussing its basic principles and presenting its current numerical and theoretical …
discussing its basic principles and presenting its current numerical and theoretical …
Explicit solvation matters: Performance of QM/MM solvation models in nucleophilic addition
JM Boereboom, P Fleurat-Lessard… - Journal of chemical …, 2018 - ACS Publications
Nucleophilic addition onto a carbonyl moiety is strongly affected by solvent, and correctly
simulating this solvent effect is often beyond the capability of single-scale quantum …
simulating this solvent effect is often beyond the capability of single-scale quantum …