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gromacs-protein-analysis

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Protein MD analysis workflows for GROMACS.

Data & Analytics#PCA#GROMACS#MD analysis#RMSD#RMSF#DCCM#FEL
AuthorCharlesHahn
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill provides ready-to-use workflows to analyze protein molecular dynamics trajectories generated by GROMACS, turning raw simulation data into actionable insights.

Core Features & Use Cases

  • PBC correction, RMSD, RMSF, Gyrate, and SASA analyses to assess stability and folding
  • DCCM, RDCM, PCA, and FEL workflows to study correlated motions and conformational landscapes
  • Visualization and reporting: generate plots and summary metrics for publication-ready results
  • Use Case: Evaluate the stability of a protein domain across different simulation conditions and compare conformational states.

Quick Start

Ask the agent to run a full protein MD analysis on a GROMACS trajectory (md.xtc) using topology (md.tpr) and output the key results, including rmsd.xvg, gyrate.xvg, dccm.xpm, and fel.xpm.

Dependency Matrix

Required Modules

None required

Components

references

💻 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: gromacs-protein-analysis
Download link: https://github.com/CharlesHahn/DuIvySkills/archive/main.zip#gromacs-protein-analysis

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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