mdanalysis
CommunityAnalyze molecular dynamics trajectories.
Education & Research#trajectory analysis#biophysics#rmsd#computational chemistry#molecular dynamics#mdanalysis#rmsf
Authortondevrel
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill simplifies the complex task of analyzing molecular dynamics (MD) simulation trajectories, allowing researchers to extract meaningful insights from simulation data.
Core Features & Use Cases
- Trajectory Loading & Manipulation: Read and process various MD trajectory file formats (DCD, XTC, etc.).
- Structural Analysis: Perform calculations like RMSD, RMSF, distance, angle, and dihedral analysis.
- Use Case: After running a molecular dynamics simulation of a protein, use this Skill to calculate the Root Mean Square Deviation (RMSD) over time to assess its stability and conformational changes.
Quick Start
Use the mdanalysis skill to load the topology 'protein.pdb' and trajectory 'trajectory.dcd' and calculate the backbone RMSD.
Dependency Matrix
Required Modules
None requiredComponents
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: mdanalysis Download link: https://github.com/tondevrel/scientific-agent-skills/archive/main.zip#mdanalysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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