Calculating Free-Energy Differences Using an Average Force: A Tutorial for Adaptive Biasing Force Simulations The purpose of this tutorial is to get the reader familiarized with the calculation of a free-energy change along a reaction-coordinate (RC) model through a number of applications of variants of the importance-sampling adaptive biasing force algorithm. The reversible sodium-chloride ion pairing in aqueous solution serves as an introductory example, wherein the RC model is defined as the distance separating the ions. For the reversible folding of the short peptide deca-alanine, alternative collective variables are considered to map the conformational free-energy landscape. The importance-sampling algorithm is then applied to the transfer of an ethanol molecule across the water liquid–vapor interface to estimate its hydration free energy. The results are compared to those of an alchemical transformation using free-energy perturbation calculations. In the final application, the Ramachandran free-energy surface underlying the conformational equilibrium of N-methyl-N′-acetylalanylamide is determined in two dimensions, comparing single- and multiple-walker strategies.

Did you ever want to try out enhanced sampling with ABF? Have a look at our newest tutorial to get started!
doi.org/10.1021/acs....

@radutalmazan.bsky.social, Haohao Fu, Mengchen Zhou, Jérôme Hénin, James C. Gumbart and Christophe Chipot

30.09.2025 11:49 — 👍 4    🔁 3    💬 0    📌 0

Iterative variational learning of committor-consistent transition pathways using artificial neural networks - Nature Computational Science A neural network approach grounded in transition-path theory is shown to uncover committor-consistent transition pathways, resolving competing mechanisms across dynamical regimes and advancing the mod...

Out now! Chrisophe Chipot and colleagues develop a neural-network approach for committor-consistent enhanced-sampling simulations of rare events.
www.nature.com/articles/s43...
🔓https://rdcu.be/evcjW

07.07.2025 17:08 — 👍 6    🔁 3    💬 1    📌 0

White and grey topography

🚨Our July issue is now live and includes research on adverse drug reactions, multi-fidelity Bayesian optimization, rare event sampling, and much more!
t.co/myy3LVRjGO

25.07.2025 11:37 — 👍 7    🔁 2    💬 0    📌 0