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Updated: Aug 9, 2025

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments
Published on: February 4, 2021
Critical comparison of general-purpose collective variables for crystal nucleation
Julien Lam1,2, Fabio Pietrucci3
1CEMES, Centre National de la Recherche Scientifique and Université de Toulouse, 29 rue Jeanne Marvig, 31055 Toulouse Cedex, France.
Abstract:
The nucleation of crystals is a prominent phenomenon in science and technology that still lacks a full atomic-scale understanding. Much work has been devoted to identifying order parameters able to track the process, from the inception of early nuclei to their maturing to critical size until growth of an extended crystal. We critically assess and compare two powerful distance-based collective variables, an effective entropy derived from liquid state theory and the path variable based on permutation invariant vectors using the Kob-Andersen binary mixture and a combination of enhanced-sampling techniques. Our findings reveal a comparable ability to drive nucleation when a bias potential is applied, and comparable free-energy barriers and structural features. Yet, we also found an imperfect correlation with the committor probability on the barrier top which was bypassed by changing the order parameter definition.
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