AD
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Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein s…
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数据与复现
MO
molecular-dynamics
维护者 Kuan-lin Huang · 最近更新 2026年4月1日
Molecular dynamics (MD) simulation computationally models the time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools: - **OpenMM** (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support - **MDAnalysis** (https://mdanalysis.org/): Python library for reading, writing, and analy.
原始来源
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/molecular-dynamics
- 维护者
- Kuan-lin Huang
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- OpenMM (https：//openmm.org/)：High-performance MD 模拟 engine ，支持 GPU support，Python API，、 flexible force field support。
- MDAnalysis (https：//mdanalysis.org/)：Python 库 ，用于 reading，writing，、 analyzing MD trajectories ，面向 all major 模拟 packages。
- Molecular dynamics (MD) 模拟 computationally models time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools：。
- OpenMM (https：//openmm.org/)：High-performance MD 模拟 engine ，支持 GPU support，Python API，、 flexible force field support MDAnalysis (https：//mdanalysis.org/)：Python 库 ，用于 reading，writing，、 analyzing MD trajectories ，面向 all major 模拟 packages。
- Installation：```bash conda install -c conda-forge openmm mdanalysis nglview。
原始文档
SKILL.md 摘录
When to Use This Skill
Use molecular dynamics when:
- Protein stability analysis: How does a mutation affect protein dynamics?
- Drug binding simulations: Characterize binding mode and residence time of a ligand
- Conformational sampling: Explore protein flexibility and conformational changes
- Protein-protein interaction: Model interface dynamics and binding energetics
- RMSD/RMSF analysis: Quantify structural fluctuations from a reference structure
- Free energy estimation: Compute binding free energy or conformational free energy
- Membrane simulations: Model proteins in lipid bilayers
- Intrinsically disordered proteins: Study IDR conformational ensembles
Force Field Selection Guide
| System | Recommended Force Field | Water Model |
|---|---|---|
| Standard proteins | AMBER14 (amber14-all.xml) | TIP3P-FB |
| Proteins + small molecules | AMBER14 + GAFF2 | TIP3P-FB |
| Membrane proteins | CHARMM36m | TIP3P |
| Nucleic acids | AMBER99-bsc1 or AMBER14 | TIP3P |
| Disordered proteins | ff19SB or CHARMM36m | TIP3P |
pip install openff-toolkit
from openff.toolkit import Molecule, ForceField as OFFForceField from openff.interchange import Interchange
def parameterize_ligand(smiles, ff_name="openff-2.0.0.offxml"): """Generate GAFF2/OpenFF parameters for a small molecule.""" mol = Molecule.from_smiles(smiles) mol.generate_conformers(n_conformers=1)
off_ff = OFFForceField(ff_name)
interchange = off_ff.create_interchange(mol.to_topology())
return interchange
适用场景
- **Protein stability analysis**：How does mutation affect protein dynamics。
- **Drug binding 模拟s**：Characteri。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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