Which Analysis Should I Run?

You already have trajectories. This page helps you choose the analysis plugins that match the question you want to answer.

Environment Setup

All commands below assume you have activated the PolyzyMD pixi environment:

pixi shell -e build

Alternatively, prefix each command with pixi run -e build.

Quick Recommendation

If you are new to PolyzyMD or doing routine characterization, start with:

rmsd — overall structural stability over time
rmsf — per-residue flexibility
contacts — polymer-protein interactions (if polymer is present)
secondary_structure — fold integrity

This set gives a useful first pass before you move to more specialized analyses.

Question-to-plugin chooser

Question	Recommended plugins
Is my protein stable?	`rmsd`, `rmsf`, `secondary_structure`
Does the polymer interact with the protein?	`contacts`, `hydrogen_bonds`
Which residues interact with the polymer?	`contacts`, `hydrogen_bonds`
Is the active site accessible?	`sasa`, `catalytic_triad`
Does the polymer shield the protein surface?	`sasa`
Are catalytic residues properly positioned?	`catalytic_triad`, `distances`
Is a specific atom-pair distance maintained?	`distances`
How compact is the protein?	`rg`
Does the polymer bridge different protein regions?	`polymer_bridging` (experimental)
What is the interaction energy with each contact?	`binding_free_energy` (experimental)
What is the overall polymer-protein affinity?	`polymer_affinity` (experimental)
How does active-site exposure change over time?	`exposure` (experimental)

Plugin quick reference

Plugin	Stable?	Cost	Input needed
`rmsd`	✓	Low	Atom selection
`rg`	✓	Low	Atom selection
`rmsf`	✓	Low	Atom selection
`secondary_structure`	✓	Low	(uses protein by default)
`contacts`	✓	Medium	Polymer + protein selections
`distances`	✓	Low	Atom pairs
`catalytic_triad`	✓	Low	Residue pairs + threshold
`sasa`	✓	High	Target + context selections
`hydrogen_bonds`	✓	High	Groups + summaries
`binding_free_energy`	Experimental	High	Polymer + protein selections
`exposure`	Experimental	Medium	Active-site selection
`polymer_affinity`	Experimental	Medium	Polymer + protein selections
`polymer_bridging`	Experimental	Medium	Polymer + protein selections

Run multiple plugins in one pass

You can enable multiple plugins in the same comparison.yaml file:

plugins:
  rmsd:
    runs:
      - label: "Protein Backbone"
        selection: "protein and name CA"
  rmsf:
    selection: "protein and name CA"
  contacts: {}
  secondary_structure: {}

Then run all configured plugins at once:

polyzymd compare run-all