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Molecular Dynamics (OpenMM + MDAnalysis)

Set up, run, and analyze protein/ligand MD simulations end-to-end with OpenMM and MDAnalysis.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Prepares systems from PDB files: hydrogen addition, 10 Å solvent padding, 150 mM ionic strength, PME electrostatics.
  • Provides the standard pipeline as ready-to-run functions: energy minimization → NVT equilibration → NPT production, with GPU (CUDA/OpenCL) fallback and checkpointing.
  • Analyzes trajectories with MDAnalysis: RMSD time series, per-residue RMSF, protein–ligand contact tracking, and matplotlib plots.
  • Includes a force-field selection table by system type, PDBFixer preprocessing, and OpenFF/GAFF2 ligand parameterization.

Who it's for

  • Structural biologists, computational chemists, and bioinformatics grad students.
  • Drug discovery teams validating ligand binding modes and stability.
  • Anyone quantifying how a mutation changes protein flexibility.

Examples

  1. "Clean this PDB with PDBFixer and run a 1 ns NPT simulation using amber14 + TIP3P-FB."
  2. "Compute backbone RMSD and per-residue RMSF from npt_traj.dcd and plot them."
  3. "List residues within 4.5 Å of the ligand (resname LIG) for each frame of the trajectory."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/molecular-dynamics/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/molecular-dynamics folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/molecular-dynamics/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/molecular-dynamics ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy this skill only: cp -r scientific-agent-skills/skills/molecular-dynamics ~/.claude/skills/
  4. Install the scientific stack: conda install -c conda-forge openmm mdanalysis nglview pdbfixer
  5. For GPU runs, verify your CUDA driver and check platforms with python -m openmm.testInstallation.
  6. Restart Claude Code, then ask something like "prepare an MD simulation for this PDB" to trigger the skill.
View source on GitHub ↗License: MIT