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2D Density Map#

The 2D density map analysis combines two saved scalar analyses into a two-dimensional density estimate. It is useful for discovering preferred regions in a reduced coordinate space defined by observables that matter to you.

Path Analyzer - 2D density map

Adding the plot#

  1. Open Path Analyzer.
  2. Create or reuse two saved scalar analyses in the Analysis Tray.
  3. Choose 2D density map in Observable.
  4. Select exactly two saved scalar analyses in the tray.
  5. Click Add Density Map.

Inputs#

  • This is a derived analysis: it uses the Analysis Tray instead of direct atom selections.
  • The two source analyses must be frame-wise scalar analyses computed on the same path.

View#

  • 2D density map: a heatmap showing where the path spends most of its time in the chosen two-observable space.

Key equation#

If \(n_{mn}\) points fall into the \((m,n)\)-th bin of width \(\Delta x\) by \(\Delta y\), Path Analyzer displays the normalized bin density

\[ \rho_{mn}=\frac{n_{mn}}{N\,\Delta x\,\Delta y} \]

where \(N\) is the total number of sampled frame-wise points.

Tip

  • Choose observables that capture orthogonal aspects of the motion, for example Distance vs RMSD, or Radius of gyration vs Energy.
  • Density maps summarize sampling density, not energy.
  • If you want the same two-observable projection colored by energy, use Energy landscape.