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molecular-dynamics

Maintainer Kuan-lin Huang · Last updated April 1, 2026

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.

Claude CodeOpenClawNanoClawAnalysisReproductionmolecular-dynamicsbioinformaticsanalysisanalysis & methodology

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/molecular-dynamics

Maintainer: Kuan-lin Huang
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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 analyzing MD trajectories from all major simulation packages.
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 analyzing MD trajectories from all major simulation packages.
Installation: ```bash conda install -c conda-forge openmm mdanalysis nglview.

Source Doc

Excerpt From SKILL.md

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

Use cases

**Protein stability analysis**: How does a mutation affect protein dynamics?
**Drug binding simulations**: Characteri.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

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