activity-log

Use when submitting or reviewing batch Jobs that need on-demand GPU/TPU capacity on Kubernetes via Kueue and a dynamic provisioning scheduler (e.g.

Oversight review for quality, simplicity, and documentation.

Shared team graph memory — record and recall lessons, patterns, gotchas, and decisions across runs.

Use when you need a decision, clarification, or approval from the user, and to decide when to instead proceed autonomously.

Use when analyzing molecular dynamics trajectories — RMSD/RMSF, clustering, contacts, hydrogen bonds, or convergence (MDAnalysis or GROMACS tools).

Use when computing binding or conformational free energies, or accelerating sampling beyond plain MD (FEP, TI, umbrella sampling, metadynamics, GaMD, MM/PBSA).

Use when writing or reviewing Kubernetes manifests or deploying workloads to a cluster.

Use when setting up, running, or reviewing a classical molecular dynamics simulation (GROMACS, NAMD, OpenMM, or AMBER).

Use when adding logging, metrics, or tracing to code or services.

Use when there is a stated performance concern or a measured bottleneck — not by default.

Use when designing or fixing CI/CD pipelines such as GitHub Actions.

Use when you have a written, approved implementation plan to execute step by step with review checkpoints.