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 …
Tracking the delocalized proton in concerted proton transfer in bulk water
A solvated proton in water is often characterized as a charge or structural defect, and it is
important to track its evolution on-the-fly in certain dynamics simulations. Previously, we …
important to track its evolution on-the-fly in certain dynamics simulations. Previously, we …
Adaptive-partitioning multilayer dynamics simulations: 2. Implementations of the permuted and interpolated adaptive-partitioning gradients
Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1
and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the …
and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the …
Adaptive partitioning QM/MM for molecular dynamics simulations: 6. Proton transport through a biological channel
Adaptive quantum-mechanics/molecular-mechanics (QM/MM) dynamics simulations feature
on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories …
on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories …
Tracking proton transfer through titratable amino acid side chains in adaptive QM/MM simulations
Ubiquitous throughout biological processes, proton transport usually occurs through the
Grotthuss shuttling mechanism, where the hydrated proton exists as a charge or structural …
Grotthuss shuttling mechanism, where the hydrated proton exists as a charge or structural …
Adaptive QM/MM for molecular dynamics simulations: 5. On the energy-conserved permuted adaptive-partitioning schemes
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 …
the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth …
Adaptive-partitioning multilayer dynamics simulations: 1. On-the-fly switch between two quantum levels of theory
We propose to generalize the previously developed two-layer permuted adaptive-
partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms …
partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms …
Resha** the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water
Adaptive quantum mechanics/molecular mechanics (QM/MM) reclassifies on-the-fly a
molecule or molecular fragment as QM or MM during dynamics simulations without abrupt …
molecule or molecular fragment as QM or MM during dynamics simulations without abrupt …
A benchmark study of kinetic isotope effects and barrier heights for the Finkelstein reaction
S Zaczek, F Gelman… - The Journal of Physical …, 2017 - ACS Publications
Herein, we present a combined (experimental and computational) study of the Finkelstein
reaction in condensed phase, where bromine is substituted by iodine in 2 …
reaction in condensed phase, where bromine is substituted by iodine in 2 …
On-the-fly determination of active region centers in adaptive-partitioning QM/MM
Z Yang - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
Quantum mechanics/molecular mechanics (QM/MM) methods are widely used in molecular
dynamics (MD) simulations of large systems. By partitioning the system into active and …
dynamics (MD) simulations of large systems. By partitioning the system into active and …