  Free energy landscapes provide insights into conformational ensembles of
biomolecules. In order to analyze these landscapes and elucidate mechanisms
underlying conformational changes, there is a need to extract metastable states
with limited noise. This has remained a formidable task, despite a plethora of
existing clustering methods. We present InfleCS, a novel method for extracting
well-defined core states from free energy landscapes. The method is based on a
Gaussian mixture free energy estimator and exploits the shape of the estimated
density landscape. The core states that naturally arise from the clustering
allow for detailed characterization of the conformational ensemble. The
clustering quality is evaluated on three toy models with different properties,
where the method is shown to consistently outperform other conventional and
state-of-the-art clustering methods. Finally, the method is applied to a
temperature enhanced molecular dynamics simulation of Ca2+ bound Calmodulin.
Through the free energy landscape, we discover a pathway between a canonical
and a compact state, revealing conformational changes driven by electrostatic
interactions.
