RMSD (pairwise)#
RMSD (pairwise) compares every frame with every other frame and displays the result as a heatmap. It is especially useful for spotting blocks of similar conformations, transitions, or recurring states.
Adding the plot#
- Open Path Analyzer.
- Choose RMSD (pairwise) in Observable.
- Choose a Path.
- Define a Measured set and a Fit set.
- Click Add Heatmap.
Inputs#
- Two atom-containing selections are required.
- As for RMSD, the fit set controls how each frame pair is aligned before the measured set is compared.
View#
- Heatmap: a square matrix where each cell reports the RMSD between two frames.
Key equation#
For every pair of frames \(i\) and \(j\), Path Analyzer aligns the fit set of one frame onto the other and computes
\[
\operatorname{RMSD}_{ij}=
\sqrt{
\frac{1}{N}
\sum_{k=1}^{N}
\left\|
\tilde{\mathbf{r}}^{(i\to j)}_k-\mathbf{r}^{(j)}_k
\right\|^2
}
\]
The resulting matrix is symmetric and is displayed as the heatmap.
Interactions#
- Clicking a heatmap cell moves the path to the later of the two selected frames.
Tip
- Use pairwise RMSD when a single reference frame is not enough.
- Large low-RMSD blocks often correspond to metastable states or structurally similar phases.
- Combine the result with Energy landscape or Custom scatter when you want a complementary low-dimensional view.