菜单
Plan and review molecular dynamics simulations and trajectory analysis with OpenMM, GROMACS, AmberTools, MDAnalysis, MDTraj, and reproducibility checks. Use when users ask about MD setup, force fields, equilibration, production runs, trajectories, RMSD/RMSF, or binding/stability dynamics.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Plan and review computational fluid dynamics workflows with meshes, boundary conditions, turbulence models, OpenFOAM/FluidSim-style solvers, validation cases, convergence checks, and reproducible simulation artifacts. Use when users mention CFD, fluid dynamics, Navier-Stokes, meshing, turbulence, OpenFOAM, or flow simulation.
Run evaluator-driven hypothesis trees for improving research artifacts, prompts, analyses, and designs. Use when a task needs branch-and-prune exploration, rubric scoring, iterative refinement, or explicit comparison of competing scientific/workflow alternatives.
Detect repeated user workflows and draft native BioRouter skills, hooks, or checklist updates from observed work patterns. Use when users ask to turn repeated work, screen-history patterns, project routines, or recurring guardrails into reusable BioRouter skills.
Plan and audit BIDS neuroimaging datasets, derivatives, validation, metadata, and reproducible preprocessing. Use when users mention BIDS, fMRI, MRI, EEG/MEG/iEEG, DICOM conversion, dataset_description.json, participants.tsv, or neuroimaging derivatives.
Plan and review clinical AI modeling workflows with EHR cohorts, PyHealth-style tasks, validation, bias checks, calibration, safety boundaries, and no-PHI handling. Use when users ask about clinical prediction models, risk scores, treatment-response ML, medical reports, or clinical model evaluation.
Plan and review general time-series forecasting with classical models, ML, foundation models, backtesting, leakage checks, and uncertainty. Use for non-omics forecasting, sensor streams, operations, finance, clinical vitals, demand, or irregular temporal data.
| name | molecular-dynamics |
| description | Plan and review molecular dynamics simulations and trajectory analysis with OpenMM, GROMACS, AmberTools, MDAnalysis, MDTraj, and reproducibility checks. Use when users ask about MD setup, force fields, equilibration, production runs, trajectories, RMSD/RMSF, or binding/stability dynamics. |
| user-invocable | true |
| license | Apache-2.0 |
Source adaptation: BioRouter-original synthesis inspired by Scientific Agent Skills molecular-dynamics patterns, rewritten under Apache-2.0.
Use this skill for molecular dynamics setup, execution planning, or trajectory analysis. Prefer ProteinStructureAgent, ChemoinformaticsAgent, RowanMolecularModelingAgent, or TamarindBioAgent when live structure/platform data or cloud jobs are needed.
Collect:
Do not overclaim from MD:
Return: system summary, setup plan, execution commands or pseudocode, analysis plan, expected artifacts, and validation risks.
