scientific-md-simulation
CommunityAnalyze MD simulations with MDAnalysis & OpenFF.
Authornahisaho
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Analyze and interpret molecular dynamics trajectories by computing key structural metrics across time, enabling rigorous assessment of stability and interactions.
Core Features & Use Cases
- RMSD/RMSF/Rg time-series to quantify structure deviations and flexibility.
- Hydrogen bonds & SASA analyses to evaluate interactions and solvent exposure in protein-ligand systems.
- OpenFF parameterization for ligand force-field generation to support end-to-end MD workflows.
- Use Case: Assess stability of a protein-ligand complex over a 100 ns trajectory and extract per-frame metrics for publication-ready figures.
Quick Start
Run the MD analysis pipeline on your trajectory to compute RMSD, RMSF, Rg, H-bonds, and SASA.
Dependency Matrix
Required Modules
None requiredComponents
Standard packageđź’» 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: scientific-md-simulation Download link: https://github.com/nahisaho/satori/archive/main.zip#scientific-md-simulation Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.