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  • Get Started
    • Quick Install
    • Create Your First Project
    • What’s Inside config.yaml
    • Where to Go Next
      • Install PolyzyMD with pixi
      • Run Your First PolyzyMD Simulation
  • Tutorials
    • Featured Tutorials
    • What Belongs Here
      • Run Your First PolyzyMD Simulation
      • Run Your First Analysis
      • Analyze a Multi-Condition Study
      • Measure Surface Accessibility with SASA
  • How-To Guides
    • Simulation Setup
      • Add Polymers to a Simulation
      • Generate Polymers from SMILES
      • Add Distance Restraints
      • Set Up Equilibration Stages
      • Run GROMACS Simulations on HPC Clusters
    • HPC & Job Submission
      • Run Simulations on SLURM Clusters
      • Submit Analysis Jobs to SLURM
    • Stable Analysis Workflows
      • Which Analysis Should I Run?
      • Compare Simulation Conditions
      • Run RMSD Analysis
      • Run Rg Analysis
      • Run RMSF Analysis
      • Run Distance Analysis
      • Run Contacts Analysis
      • Analyze Hydrogen Bonds
      • Run Catalytic Triad Analysis
    • Experimental Analysis Workflows
      • Analyze Binding Preference
      • Analyze Binding Free Energy
      • Analyze Polymer Affinity
      • Analyze Polymer Bridging
      • Analyze Exposure Dynamics
    • Plots & Troubleshooting
      • Customizing Plots for Publication
      • Contacts Cookbook
      • Broken Molecule Debugging
      • Troubleshoot Common Problems
  • Reference
    • CLI, Configuration & Data
      • CLI Reference
      • Configuration Reference
      • Data Requirements & Directory Layout
      • Benchmarks
    • Analysis Plugin Reference
      • Comparison YAML Schema
      • Analysis Plugin Settings Reference
      • Comparison and Plotting Reference
      • RMSD Plugin Reference
      • Rg Plugin Reference
      • RMSF Plugin Reference
      • Catalytic Triad Plugin Reference
      • Distances Plugin Reference
      • Contacts Plugin Reference
      • Post-Hoc Testing Reference
    • API Reference
      • API Reference
  • Explanation
    • Concepts and Design
      • Analysis System Concepts
      • Architecture
      • Residue Assignment and Chain Conventions
      • Colored Logging
    • Interpretation and Best Practices
      • Statistical Best Practices for Analysis
      • RMSD Best Practices
      • Convergence Detection
      • Rg Best Practices
      • RMSF Best Practices
      • RMSF Reference Selection
      • RMSF Verification
      • Catalytic Triad Best Practices
    • Experimental Analysis Concepts
      • Polymer Bridging Interpretation
  • Contributor Guide
    • Start Here
    • Extension Workflows
    • Contributor Mindset
      • Contributing to PolyzyMD
      • Set Up a Contributor Environment
      • Packaging and Distribution Notes
      • Extend the Analysis Framework
      • Comparison Logic in an Analysis Plugin
      • Plotting in an Analysis Plugin
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