radutalmazan.bsky.social
@radutalmazan.bsky.social
Reposted
🚨A new QM/MM MD workflow + ML analysis reveals reaction coordinates in supramolecular catalysts as sequences of motions.

Read the full paper by @podewitzlab.bsky.social et al., from TU Wien

👉doi.org/10.1039/D5DD...

October 20, 2025 at 11:43 AM
Reposted
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
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.
doi.org
September 30, 2025 at 11:49 AM
Reposted
What happens in @chemistry-tuw.bsky.social and @universityofhawaii.bsky.social join forces?
You work on ice 🧊.
Check out our new publication on the UV-vis redshirt of carbonic acid in gas phase vs. bulk.
doi.org/10.1002/cphc...
doi.org
August 7, 2025 at 8:29 AM