mdclaw

Standalone minimization plus equilibration of a prepared MD system using MDClaw CLI tools, including low-temperature NVT warmup, NVT heating, and optional NPT density. Creates min and eq DAG nodes and writes restart artifacts for production handoff.

Molecular dynamics preparation with MDClaw CLI tools: acquisition, molecule selection, cleaning, solvation, and topology. Before any state-changing command, follow the pre-command gate in this skill; open linked pages only when their condition applies.

Production molecular dynamics simulation using MDClaw CLI tools and OpenMM. Runs MD from an equilibrated state, with HMR, restart, and HPC submission support.

SLURM-based HPC submission for MDClaw workflow nodes. Handles cluster inspection, single-node and job-array submission, status sync to the DAG, and production restart extensions.

Molecular dynamics trajectory analysis using MDClaw CLI tools. Routes concat, metric, and troubleshooting workflows through focused guidance pages.

Study-level planning and workflow routing for MDClaw. Use for scientific questions, comparative or campaign studies, plan-only requests, and requests to carry planned MD jobs through analysis to an evidence-backed answer.

Generate monomer conformational source candidates with BioEmu, then hand them to MDClaw preparation.

AI-driven protein structure prediction using Boltz-2 for single proteins, multimers, and protein-ligand complexes.

Build template-based comparative protein models with MODELLER and register them as MDClaw source candidates.