Explanation
Use Explanation when you need the reasoning behind PolyzyMD: design choices, analysis assumptions, statistical interpretation, and plugin-specific caveats. If you want commands for a task, start with How-To Guides. If you need to look up options, file layouts, or schemas, use Reference.
Tip
New to the analysis plugin system? Start with Analysis System Concepts, then read the statistical and reference-selection pages listed in the contributor pathway below.
Read the concepts, statistics, convergence, and reference-selection pages that shape analysis-plugin design.
Understand replication, uncertainty, multiple comparisons, and convergence before comparing simulation conditions.
Learn why RMSF depends on alignment, residue mapping, replicate treatment, and the selected structural reference.
See the design rationale and implementation constraints that keep PolyzyMD analyses consistent. Chain conventions are covered in the residue-assignment page.
New contributor pathway
If you are adding or reviewing an analysis plugin, read these pages first:
Analysis System Concepts for the analysis lifecycle and plugin boundaries.
Statistics Best Practices for MD Analysis for replicate-level interpretation and statistical expectations.
Establishing Convergence in MD Simulations for deciding whether trajectory summaries are interpretable.
How RMSF reference selection changes interpretation for how structural references affect RMSF and related fluctuation metrics.
Concepts and Design
Interpretation and Best Practices
Start with the cross-cutting interpretation pages, then use the plugin-specific pages for caveats tied to particular metrics.