NetMD is a computational method for identifying consensus behavior across multiple molecular dynamics simulations.
Using Graph-based Embeddings and Dynamic Time Warping, NetMD aligns trajectories that may be temporally out of sync and pinpoints the replicas that most faithfully represent the overall ensemble behavior. This enables consistent comparisons across simulations and supports reliable characterization of system variants, making it easier to detect shared patterns and reduce the influence of outliers or simulation artifacts.
