Abstract
A major challenge in applying the weighted ensemble enhanced sampling strategy to simulate a rare-event process of interest is to identify an effective progress coordinate. Furthermore, the algorithm for the resampling procedure of the strategy can impact both the number and diversity of representative pathways generated. Here, I will share lessons learned from the application of atomistic, weighted ensemble simulations to a surprisingly challenging protein-ligand unbinding process that features a highly-charged ligand. These lessons include key considerations regarding the choice of progress coordinate and resampling algorithm, including binless resamplers.
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