Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning

J Phys Chem Lett. 2024 Feb 15;15(6):1774-1783. doi: 10.1021/acs.jpclett.3c03542. Epub 2024 Feb 8.

Abstract

Enhanced-sampling algorithms relying on collective variables (CVs) are extensively employed to study complex (bio)chemical processes that are not amenable to brute-force molecular simulations. The selection of appropriate CVs characterizing the slow movement modes is of paramount importance for reliable and efficient enhanced-sampling simulations. In this Perspective, we first review the application and limitations of CVs obtained from chemical and geometrical intuition. We also introduce path-sampling algorithms, which can identify path-like CVs in a high-dimensional free-energy space. Machine-learning algorithms offer a viable approach to finding suitable CVs by analyzing trajectories from preliminary simulations. We discuss both the performance of machine-learning-derived CVs in enhanced-sampling simulations of experimental models and the challenges involved in applying these CVs to realistic, complex molecular assemblies. Moreover, we provide a prospective view of the potential advancements of machine-learning algorithms for the development of CVs in the field of enhanced-sampling simulations.

Publication types

  • Review

MeSH terms

  • Algorithms*
  • Entropy
  • Humans
  • Machine Learning
  • Molecular Dynamics Simulation*
  • Prospective Studies