Logo
  • Get Started
    • Quick Install
    • Create Your First Project
    • What’s Inside config.yaml
    • Where to Go Next
      • Install PolyzyMD with pixi
        • Before You Start
        • 1. Install pixi
        • 2. Install on a Local Machine
        • 3. If You Are Installing on HPC
        • 4. Verify the Commands You Can Use
        • Common Installation Checks
        • Contributor Setup
        • Next Step
      • Run Your First PolyzyMD Simulation
        • What You Will Learn
        • Prerequisites
        • Step 1: Create a new project scaffold
        • Step 2: Add your enzyme structure
        • Step 3: Replace the template with a minimal config
        • Step 4: Validate the config
        • Step 5: Check that the system can build
        • Step 6: Decide how you want to run production
        • What you should have now
        • Step 7: Monitor progress
        • Where to go next
  • Tutorials
    • Featured Tutorials
    • What Belongs Here
      • Run Your First Analysis
        • What You Will Learn
        • Prerequisites
        • Step 1: Create a Comparison Project
        • Step 2: Edit comparison.yaml
        • Step 3: Run RMSF Analysis
        • Step 4: Find Your Results
        • Step 5: Add Plotting (Optional)
        • What’s Next
      • Prepare a PDB for OpenFF and PolyzyMD
        • What you will produce
        • Prerequisites
        • Inspect the raw 4CHA biological contents
        • Preview the system selection in PyMOL
        • Add hydrogens and write the PolyzyMD PDB
        • Validate the prepared file with OpenFF
        • What curate upstream means
        • Use the validated PDB in PolyzyMD
        • Why not just run polyzymd clean-pdb?
      • Analyze a Multi-Condition Study
        • What You Will Learn
        • Prerequisites
        • The Study We Will Analyze
        • Step 1: Create the Comparison Workspace
        • Step 2: Validate the Comparison Config
        • Step 3: Run the Cross-Condition Comparison
        • Step 4: Generate the Figures
        • What Success Looks Like
        • What to Do Next
      • Measure Surface Accessibility with SASA
        • Prerequisites
        • What SASA will tell us
        • Step 1: Add paired SASA runs
        • Step 2: Use the runs in a comparison file
        • Step 3: Run the SASA analysis
        • Step 4: Check that the run succeeded
        • Step 5: Interpret the shielding signal
        • Step 6: Use the plots
        • What you have now
        • Next steps
  • How-To Guides
    • Simulation Setup
      • Add Polymers to a Simulation
        • Overview
        • Basic Configuration
        • Monomer Definition
        • Chain Configuration
        • Pre-Built Polymer SDFs
        • Polymer Cache
        • Example Configurations
        • Disabling Polymers
        • Placement and Solvation
        • Troubleshooting
        • Performance Considerations
        • See Also
      • Generate Polymers from SMILES
        • Overview
        • When to Use Dynamic Mode
        • Quick Start
        • Configuration Reference
        • Complete Example Configuration
        • How Dynamic Generation Works
        • Supported Chemistries
        • Troubleshooting
        • Performance Tips
        • See Also
      • Add Distance Restraints
        • Step 1: choose the restraint type
        • Step 2: add the restraint to config.yaml
        • Step 3: make selections specific
        • Step 4: find the right atom indices
        • Step 5: validate and test
        • Common patterns
        • Force constant starting points
        • Troubleshooting
        • Related pages
      • Set Up Equilibration Stages
        • When to use staged equilibration
        • Basic rule
        • Simple three-stage example
        • How to choose stage settings
        • Common recipes
        • Validate the setup
        • Outputs to expect
        • Troubleshooting
        • Related pages
      • Run GROMACS Simulations on HPC Clusters
        • Quick Start: CPU
        • Build-only GROMACS export
        • Quick Start: GPU
        • GROMACS Flag Glossary
        • Understanding MPI vs OpenMP Parallelism in GROMACS
        • Complete gromacs: Config Reference
        • SBATCH to PolyzyMD YAML Mapping
        • Cluster Recipes
        • GPU Constraints and Preemption
        • Recovering Preempted Jobs
        • GROMACS Output Files
        • Troubleshooting
        • See Also
    • HPC & Job Submission
      • Run Simulations on SLURM Clusters
        • Before you start
        • Step 1: validate and dry-run locally
        • Step 2: pick a preset
        • Step 3: submit one small test job
        • Step 4: submit your real run
        • Monitor jobs
        • Recover a stalled replicate
        • Cluster-specific note for Bridges2
        • Cluster-specific note for CU Boulder (Alpine and Blanca)
        • What the generated scripts do
        • GROMACS engine
        • Common fixes
        • Related reference pages
      • Submit Analysis Jobs to SLURM
        • Before You Start
        • What the DAG Looks Like
        • Submitting all enabled analyses with dependency ordering
        • Framework finalize-only mode
        • The Example Study
        • Step 1: Dry Run
        • Step 2: Submit the DAG
        • Step 3: Monitor Progress
        • Step 4: Finalize Results
        • Troubleshooting
        • Resource Configuration Reference
        • CU Boulder HPC: Alpine and Blanca
        • What You Have Now
        • See Also
    • Stable Analysis Workflows
      • Which Analysis Should I Run?
        • Quick Recommendation
        • Question-to-plugin chooser
        • Plugin quick reference
        • Run multiple plugins in one pass
        • See Also
      • Compare Simulation Conditions
        • Before You Start
        • Step 1: Create a Comparison Workspace
        • Step 2: Define a Minimal comparison.yaml
        • Step 3: Validate the Config
        • Step 4: Run One Comparison
        • Step 5: Run All Enabled Comparisons
        • Step 6: Generate Figures
        • Step 7: Check the Outputs
        • Programmatic Use
        • Adding More Stable Analyses
        • Troubleshooting
        • See Also
      • Run RMSD Analysis
        • TL;DR
        • Prerequisites
        • What RMSD Analysis Provides
        • Basic Usage
        • Multi-Run Configuration
        • External Reference Mode
        • Comparing RMSD Across Conditions
        • Reference and Troubleshooting
        • Next Steps
      • Run Rg Analysis
        • TL;DR
        • Prerequisites
        • What Rg Analysis Provides
        • Basic Usage
        • Multi-Run Configuration
        • Key Mode: Fragment-Aware Rg
        • Comparing Rg Across Conditions
        • Reference and Troubleshooting
        • Next Steps
      • Run RMSF Analysis
        • TL;DR
        • Prerequisites
        • What RMSF gives you
        • Set up comparison.yaml
        • Run RMSF
        • Compare conditions
        • Comparing Two Conditions
        • Common task patterns
        • Python API (programmatic run)
        • Where to find details
        • Next steps
      • Run Distance Analysis
        • TL;DR
        • Prerequisites
        • What Distance Analysis Provides
        • Basic Usage
        • Add Contact-Style Thresholds
        • Write Robust Selections
        • Use PBC and Alignment Defaults
        • Compare Distances Across Conditions
        • Reference and Troubleshooting
        • Next Steps
      • Run Contacts Analysis
        • TL;DR
        • Prerequisites
        • Chain convention used by contacts
        • Basic usage
        • Key metrics to check first
        • Common tasks
        • Quick output checks
        • Programmatic post-processing (JSON)
        • Compare conditions
        • Reference and troubleshooting
        • Next steps
      • Run SASA Analysis
        • TL;DR
        • Prerequisites
        • Configure a minimal whole-protein run
        • Configure a two-run shielding comparison
        • Focus on active-site exposure
        • Compare monomer-specific shielding
        • Use stride and chunking for long trajectories
        • Run on SLURM instead of locally
        • Generate plots after a completed run
        • Quick output checks
        • Common fixes
        • Where to find details
      • Analyze Hydrogen Bonds
        • When to Use This Plugin
        • Before You Start
        • Quick Start
        • Configuration Reference
        • Common Recipes
        • Running the Analysis
        • Understanding the Output
        • Interpreting the Plots
        • Scientific Considerations
        • Full Example: comparison.yaml
        • CLI name
        • See Also
      • Run Catalytic Triad Analysis
        • TL;DR
        • Prerequisites
        • What Catalytic Triad Analysis Provides
        • Basic Usage
        • Selection Rules That Prevent Most Errors
        • Comparing Conditions
        • Reference and Troubleshooting
        • Next Steps
    • Plots & Troubleshooting
      • Customizing Plots for Publication
        • The plot_settings block
        • Use semantic colors for condition series
        • Changing output format
        • Changing DPI
        • Per-plugin plot settings
        • Re-generating plots after changing settings
        • See Also
      • Create Custom Plots from Analysis Artifacts
        • Prepare a notebook context cell
        • Import notebook dependencies
        • Set the project paths and summaries
        • Validate that expected artifacts exist
        • Load and validate hydrogen-bond artifacts
        • Extract a tidy DataFrame
        • Plot grouped bars with SEM and replicate dots
        • Save outside the canonical analysis tree
        • Adapt this pattern
        • Troubleshoot common notebook issues
        • See also
      • Broken Molecule Debugging
        • TL;DR (The Quick Fix)
        • The Problem We Encountered
        • Background: How DCD Trajectories Work
        • Our Debugging Journey
        • Root Cause: Atom Order Mismatch
        • The Solution
        • Lessons for Future Developers
        • How to Verify the Fix Worked
        • Appendix: Technical Details
      • Troubleshoot Common Problems
        • Installation Issues
        • Configuration Errors
        • System Building Errors
        • Simulation Errors
        • SLURM/HPC Errors
        • Continuation Errors
        • Visualization Issues
        • Known Limitations
        • Submission Issues
        • Getting Help
  • Reference
    • CLI, Configuration & Data
      • CLI Reference
        • Global Options
        • polyzymd init
        • polyzymd validate
        • polyzymd build
        • polyzymd run
        • polyzymd submit
        • polyzymd run-segment
        • polyzymd check-progress
        • polyzymd status
        • polyzymd recover
        • polyzymd info
        • polyzymd new-analysis
        • polyzymd compare
        • Plotting comparisons (polyzymd compare plot-all)
        • Environment Variables
        • Exit Codes
        • See Also
      • Configuration Reference
        • Configuration Structure
        • Enzyme Configuration
        • Substrate Configuration
        • Polymer Configuration
        • Solvent Configuration
        • Restraints Configuration
        • Thermodynamics Configuration
        • Simulation Phases Configuration
        • Output Configuration
        • Force Field Configuration
        • GROMACS Engine Configuration
        • Complete Example
        • See Also
      • Data Requirements & Directory Layout
        • The Two-Project Pattern
        • Simulation Project Layout
        • Directory Naming Template
        • Scratch vs Projects Directories
        • What the Analysis Framework Expects
        • Input File Requirements
        • Comparison Project Layout
        • Connecting It All Together
        • Common Pitfalls
        • See Also
      • Benchmarks
        • How to Read These Tables
        • CU Boulder Alpine Cluster
        • Blanca Cluster
        • Benchmark Conditions
        • Contributing Benchmarks
        • Estimating Simulation Time
    • Analysis Plugin Reference
      • Comparison YAML Schema
        • Minimal Working Example
        • Top-Level Fields
        • conditions[*]
        • defaults
        • mda_backend_policy
        • plugins
        • plot_settings
      • Analysis Plugin Settings Reference
        • rmsf
        • catalytic_triad
        • distances
        • contacts
        • secondary_structure
        • sasa
        • hydrogen_bonds
        • rg
        • rmsd
      • Comparison and Plotting Reference
        • Comparison Project Layout
        • Core comparison.yaml Fields
        • Per-Plugin Statistical Settings
        • Stable Plugin Keys
        • Plugin Summary Table
        • Path Rules
        • Replicate Counts
        • Commands
        • Common Stable Commands
        • Output Locations
        • Plotting Smoke Test
        • Plugin-Specific Metadata Fields
        • Statistical Terms
      • RMSD Plugin Reference
        • Configuration Reference
        • Output Files
        • Plot Types
        • Convergence Detection
        • Common CLI Options
        • Troubleshooting
        • RMSD vs RMSF Comparison
      • Rg Plugin Reference
        • Configuration Reference
        • Fragment Mode Reference
        • Why Rg Has No Alignment or Reference Fields
        • Output Files
        • Plot Types
        • Common CLI Options
        • Troubleshooting
        • Rg vs Other Metrics
      • RMSF Plugin Reference
        • Configuration Reference
        • Output Files
        • Plot Types
        • Common CLI Options
        • Troubleshooting
      • Catalytic Triad Plugin Reference
        • Configuration Reference
        • Output Files
        • Plot Types
        • Common CLI Options
        • Troubleshooting
      • Distances Plugin Reference
        • Configuration Reference
        • Output Files
        • Plot Types
        • Common CLI Options
        • Troubleshooting
      • Contacts Plugin Reference
        • Configuration Reference
        • Output Files
        • Plot Types
        • Common CLI Options
        • Troubleshooting
      • Secondary Structure Plugin Reference
        • Settings
        • Output files
        • Plot outputs
      • SASA Plugin Reference
        • Plugin key
        • Settings
        • Target and context behavior
        • Canonical output paths
        • Artifact envelope fields
        • Loading artifacts with ArtifactStore
        • Comparison output
        • Normalized-control formula
        • Plot outputs
        • Units
        • See also
      • Hydrogen Bonds Plugin Reference
        • Settings
        • Comparison mode
        • Output files
        • Plot outputs
      • Post-Hoc Testing Reference
        • Overview
        • Available Methods
        • Configuration
        • Method Details
        • ANOVA
        • Output Fields
        • CLI Significance Markers
        • Edge Cases
        • See Also
      • Experimental Analyses Archive
        • Archived names and migration path
        • Current workflow
    • API Reference
      • API Reference
      • Package and workflow APIs
        • API Overview
        • Configuration Module
        • Builders Module
        • Simulation Module
        • Workflow Module
        • Core Module
      • Analysis APIs
        • Analyses Plugin System API
        • Analysis Base Classes
        • Analysis Shared Utilities
      • MDAnalysis extension-layer APIs
        • MDAnalysis Extension-Layer API
        • Public facade
        • Job execution
        • Frame selection
        • Plugin lifecycle and collectors
        • Artifact envelopes and store
        • Aggregation and comparison
        • Universe provenance and shared MDAnalysis primitives
  • Explanation
    • New contributor pathway
    • Concepts and Design
      • Analysis system concepts
        • The analysis pipeline
        • comparison.yaml — the control file
        • Conditions and replicates
        • Plugins — the analysis modules
        • Statistical comparison
        • Output structure
        • See also
      • Architecture and design rationale
        • The high-level shape of the project
        • Why the code is split this way
        • The current analyses/ boundary
        • How the MDAnalysis lifecycle is divided
        • Comparison infrastructure is distributed
        • Supporting packages
        • How data moves through the system
        • Design patterns you will encounter
        • Where contributors usually need to look
        • A practical mental model
        • Related pages
      • Residue assignment and chain conventions
        • The core principle: one repeat unit is one residue
        • Why default topology output can lose information
        • Chain convention
        • Polymer identity and residue numbering
        • What the convention enables
        • Generated topology behavior
        • Conceptual checklist for reviewing assignments
        • Contributor guidance
        • Summary
      • Why PolyzyMD uses colored logging
        • Color Scheme
        • Terminal Support Levels
        • Disabling Colors
        • Click-styled messages
        • Design rationale for contributors
    • Interpretation and Best Practices
      • Foundations
        • Statistics best practices for MD analysis
        • Establishing convergence in MD simulations
      • Metric and plugin caveats
        • RMSD interpretation: use, limits, and cautions
        • Rg analysis: best practices
        • RMSF analysis: statistical best practices
        • How RMSF reference selection changes interpretation
        • RMSF implementation verification
        • Catalytic triad analysis: interpretation and best practices
  • Contributor Guide
    • Start Here
    • New Analysis Contributor Path
    • Extension Workflows
    • Contributor Mindset
      • Contributing to PolyzyMD
        • Start with the contributor environment
        • What good contributions look like
        • Recommended verification commands
        • A concrete example: add a new co-solvent
        • Other common contribution areas
        • Before opening a PR
        • Related pages
      • Set Up a Contributor Environment
        • What This Environment Is For
        • 1. Clone the Repository
        • 2. Install the Build Environment
        • 3. Run the Core Contributor Checks
        • 4. Optional Tooling Notes
        • 5. Keep Your Environment Updated
        • Related Pages
      • Packaging and Distribution Notes
        • Packaging model
        • Repository layout
        • pyproject.toml
        • Pixi environments
        • Lazy imports for heavy dependencies
        • CI workflows
        • Release checklist
        • Best practices
        • See also
      • New Analysis Contributor Path
        • Start
        • Build
        • Scale
        • Verify
        • Reference
        • Public and private import guardrails
      • Extend the Analysis Framework
        • What you will build
        • Start with the scaffold
        • Public imports
        • Minimal function-adapter plugin
        • Use direct AnalysisBase-compatible jobs for frame algorithms
        • FrameSelection and backend policy
        • Artifact contract
        • Raw MDAnalysis Results mapping rule
        • Aggregation and comparison
        • Plot from artifacts only
        • Trajectory selections and lazy imports
        • Testing checklist
        • Further reading
        • Style checklist
PolyzyMD
  • Search

© Copyright 2026, Joseph R. Laforet Jr..

Built with Sphinx using a theme provided by Read the Docs.