Sampling Budget Biases Apparent Metastable-State Counts in Molecular Simulation
Tests whether apparent state counts from PCA, TICA, and VAE analyses partly reflect the number of saved frames. Controlled synthetic landscapes separate sample size effects from exploration deficits, with validation on two independent 100 ns alanine dipeptide trajectories. Submitted to JCTC on September 15, 2026; the ChemRxiv preprint is under review.























