A Note on Spectral Map

In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occurrence and the huge number of degrees of freedom in molecular systems, understanding the physical properties that drive rare events is immensely difficult. A common approach to this problem is to propose a collective variable (CV) that describes this process by a simplified representation. However, choosing CVs is not easy, as it often relies on physical intuition. Machine learning (ML) techniques provide a promising approach for effectively extracting optimal CVs from MD data. Here, we provide a note on a recent unsupervised ML method called spectral map, which constructs CVs by maximizing the timescale separation between slow and fast variables in the system.