matsunagalab
10 verified skills31 total stars
md-analyze
Molecular dynamics trajectory analysis using MDClaw CLI tools. Routes concat, metric, and troubleshooting workflows through focused guidance pages.
tools4
bioemu-sample
Generate monomer conformational source candidates with BioEmu, then hand them to MDClaw preparation.
development3
boltz-predict
AI-driven protein structure prediction using Boltz-2 for single proteins, multimers, and protein-ligand complexes.
data-ai3
hpc-run
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.
tools3
md-equilibration
Equilibration (standard staged minimization -> low-temperature NVT warmup -> NVT heating -> optional NPT density) of a prepared MD system using MDClaw CLI tools. Creates an eq node and writes restart artifacts for production handoff.
tools3
md-production
Production molecular dynamics simulation using MDClaw CLI tools and OpenMM. Runs MD from an equilibrated state, with HMR, restart, and HPC submission support.
tools3
MD Benchmark OpenRouter Matrix
Run MDAgentBench harness × OpenRouter model matrix evaluations. Use when comparing multiple agent harnesses, model slugs, or OpenRouter provider-routing settings.
data-ai3
md-prepare
Molecular dynamics simulation preparation using MDClaw CLI tools. Covers structure acquisition, protein/nucleic/ligand selection, structure cleaning, solvation, and topology generation.
tools3
md-study
Study-level planning for MDClaw. Turns scientific questions into a small MD research plan, planned jobs, analysis intent, and decision criteria before handing off to stage skills.
testing3
md-benchmark
Run MDAgentBench tasks with prompt-driven MD agents and deterministic scorer commands. Use for benchmark runs, agent submissions, and comparing MD agents.
data-ai3