Dimension reduction

A molecular dynamics trajectory with \(N\) atoms can be considered a path through \(3N\)-dimensional molecular configuration space. It remains difficult to extract important dynamics or compare trajectory similarity from such a high-dimensional space. However, collective motions and physically relevant states can often be effectively described with low-dimensional representations of the conformational space explored over the trajectory. MDAnalysis implements two methods for dimensionality reduction.

For computing similarity, see the tutorials in Trajectory similarity.

• Non-linear dimension reduction to diffusion maps