CôôrdVis-MD: From Cohorts to Conformations in Adaptive Molecular Dynamics Ensembles

Abstract

While adaptive molecular dynamics successfully escapes local minima to capture rare conformational states, it generates a branching diversity of trajectories, rendering aggregate metrics insufficient for comprehensive analysis. CôôrdVis-MD, a web-based visual analytics environment, was designed to tackle this issue. Four coordinated views connect trajectory evolution, features, events, conformational states, and molecular structure via real-time cross-filters. Cohort beeswarms and lineage trees reveal simulation hierarchies, enabling the selection of ancestors, descendants, and transition cohorts over time. 3D spatial conformations are explored through side-by-side timelines, panoramic small multiples, and hierarchical treemaps. Finally, we inspect structural features globally or individually via compact heatmaps. As a result, we present two use cases that reveal adaptive simulation artifacts within the CoVAMPnet data.