Get Started
Start Here
What You Will Accomplish
Before You Move On
Install PolyzyMD with pixi
Run Your First PolyzyMD Simulation
Tutorials
Featured Tutorials
What Belongs Here
Analyze a Multi-Condition Study
How-To Guides
Core Simulation Tasks
Analysis Tasks
Recipe Collections
Run PolyzyMD on SLURM Clusters
Add Distance Restraints
Set Up Equilibration Stages
Add Polymers to a Simulation
Generate Polymers from SMILES
Export a System to GROMACS
Troubleshoot Common Problems
Run RMSF Analysis
Run Distance Analysis
Run Contacts Analysis
Compare Simulation Conditions
Run Catalytic Triad Analysis
Experimental: Analyze Binding Preference
Experimental: Analyze Binding Free Energy
Experimental: Analyze Polymer Affinity
Experimental: Analyze Exposure Dynamics
Contacts Cookbook
Broken Molecule Debugging
Reference
User-Facing Reference
API Reference
When Not to Use This Section
CLI Reference
Configuration Reference
Comparison and Plotting Reference
Benchmarks
API Overview
Configuration API
Builders API
Simulation API
Workflow API
Core API
Analysis API
Compare API
Explanation
Concepts and Design
Analysis Interpretation and Best Practices
Experimental Analysis Concepts
Architecture
Residue Assignment and Chain Conventions
Colored Logging
Statistical Best Practices for Analysis
RMSF Best Practices
RMSF Reference Selection
RMSF Verification
Catalytic Triad Best Practices
Contributor Guide
Start Here
Extension Workflows
Contributor Mindset
Contributing to PolyzyMD
Set Up a Contributor Environment
Packaging and Distribution Notes
Extend Comparison Workflows
Extend Plotting Workflows
PolyzyMD
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