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Reactive MD (method hub)

TL;DR

This is the method hub for reactive molecular dynamics in this corpus: where and how bond-breaking or bond-forming trajectories are used in practice. It is intentionally separate from reaxff-family and protocols/reaxff-parameterization-workflow, which track parameter-set lineage and fitting workflows rather than application-side interpretation.

Scope (in / out)

In scope: corpus pages that report reactive trajectories (ReaxFF or other reactive Hamiltonians), including electrolyte decomposition, oxidation, pyrolysis, combustion, intercalation, and surface reaction use cases documented in linked paper notes.

Out of scope: force-field training history without an application trajectory (route to reaxff-family and protocols/reaxff-parameterization-workflow), and non-reactive classical MD surveys where reactivity is not central.

Routing rule (method vs lineage): - If the user asks, "What chemistry emerges in trajectories under conditions X?", start here. - If the user asks, "Which parameter set was fit to what data, and how transferable is that fit?", start at reaxff-family and then protocols/reaxff-parameterization-workflow.

How this theme is organized in the corpus

Subsections below reflect corpus organization rather than a universal taxonomy. They are intended to speed retrieval across method-first questions while preserving links back to material and domain hubs.

Literature review (this knowledge base)

Reactive MD with ReaxFF (applications)

The corpus includes large-scale pyrolysis trajectories in 2014castro-marcano-journal-of-a-pyrolysis-large-scale, oxidation and oxygen-transport behavior in 2014zou-acta-materia-molecular-dynamics, reactive silica surface chemistry in 2013muri-venue-jp3086649, and defect-mediated graphene intercalation behavior in 2022nayir-carbon-190-2-atomic-scale-probing.

Reactive MD with first-principles-based or hybrid flavors

2017liu-venue-research documents a first-principles-based reactive MD treatment for h-BN nucleation on Ni, and should be used as the detailed reference point for that Hamiltonian and validation setup.

Electrolytes and interfaces (reactive bond networks)

2018shin-physical-che-development-reaxff and 2020hossain-j-chem-phys-lithium-electrolyte-solvation anchor reactive electrolyte and interface chemistry threads in this KB. When the question is battery-context first (rather than method-first), route through batteries-interfaces-reaxff.

Combustion- and high-T organic networks

2018jain-j-phys-chem-understanding-combustion provides a combustion-oriented reactive MD entry point. For fuel-centric framing, pair with theme-combustion-flames-fuels and theme-pyrolysis-combustion-organics.

Catalytic surfaces

2015broqvist-venue-jp5b01597 anchors heterogeneous reactive surface chemistry in this corpus. For catalyst-family synthesis, use theme-catalysis-surfaces.

2D materials, water droplets, and defects

2021verma-physical-che-reaxff-reactive connects defective h-BN, water nanodroplets, and reactive ReaxFF trajectories; combine with theme-2d-epitaxy-growth and theme-water-silica-geo for material-first navigation.

Analysis and cross-cutting patterns

Across linked pages, reporting depth for timestep, ensemble control, and system size is uneven, so cross-paper comparability must be checked at the paper page level. This hub therefore summarizes where reactive MD is used, while numerical benchmarking and parameter-quality claims remain anchored to individual paper notes.

Debates, tensions, and limitations

  • Transferability of reactive models: transferability-reactive-ff, reaxff-vs-mlip-accuracy.
  • Sampling: rare events may require specialized workflows not documented on every page—do not assume single long MD trajectories suffice.
  • Method-lineage split: training or re-fitting parameters is a lineage/protocol concern, while trajectory interpretation under a chosen reactive model is a method/application concern.

Gaps and open directions (corpus view)

The corpus does not yet provide uniform coverage of accelerated sampling variants, adaptive KMC couplings, or every QM/MM reactive workflow. As method-forward paper notes are expanded, this hub should be refreshed with additional source_refs and tighter cross-links to protocol and debate pages.

Representative entry points

Methods and limitations

Reactive MD interpretation depends on the chosen reactive Hamiltonian and parameter set, so quantitative kinetics and transferability should be treated as paper-scoped unless independently validated against experiment or higher-level calculations in the linked notes.

MAS / retrieval

id: concept:theme-reactive-md-corpus. primary intent: method-first routing for reactive trajectory questions. disambiguation cues: method:reaxff + domain:reactive-md indicate application usage; lineage and fitting provenance route to reaxff-family and protocols/reaxff-parameterization-workflow. query hints: "reactive MD transferability", "bond breaking trajectory", "electrolyte decomposition reactive", "surface reaction ReaxFF", "combustion reactive trajectory". maintenance note: refresh source_refs and supported_by together when adding method-forward papers so retrieval and evidence graphs remain aligned.