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

Authors

Marcus Matheus Lameira de Araújo (Federal University of Pará), Bianchi Serique Meiguins (Federal University of Pará), Carlos Gustavo Resque dos Santos (Federal University of Pará)

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.