Michael Yang

DOI: https://doi.org/10.5281/zenodo.22258130

We present HKD-Water, a reproducible benchmark for exact incremental reevaluation of localized perturbations in a molecular-water interaction workload. The public artifact uses the rigid four-site TIP4P/2005 interaction model and compares a localized update against an independent full reevaluation after every perturbation. The scientific result is expressed in two deliberately separate metrics: measured wall-clock speedup and a machine-independent logical interaction cycle reduction. The released implementation is publication-safe: it contains the reference physics, benchmark construction, exactness test, timing harness, and cryptographic fingerprints, but no proprietary HKD indexing, persistence, dispatch, cache, or acceleration implementation. The benchmark is an interaction reevaluation experiment rather than a complete molecular-dynamics trajectory

TIP4P/2005; molecular water; incremental computation; localized perturbation; molecular simulation; exact computation

HKD-Water establishes a compact, reproducible reference experiment for exact incremental molecular-water interaction reevaluation. The public artifact memorializes the scientific claim while maintaining a strict disclosure boundary around proprietary HKD acceleration machinery. Future work can extend the same validation discipline to force and torque evaluation, neighbor-list maintenance, time integration, ensemble control, and full moleculardynamics trajectories.

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Michael Yang (2026). HKD-Water: Exact Incremental Reevaluation of Local Perturbations in a TIP4P/2005 Molecular Water Interaction Workload. International Journal of Computer Techniques, 13(4), 313–315. ISSN: 2394-2231. DOI: https://doi.org/10.5281/zenodo.22258130