Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method
Overview
Affiliations
We report a theoretical description and numerical tests of the extended-system adaptive biasing force method (eABF), together with an unbiased estimator of the free energy surface from eABF dynamics. Whereas the original ABF approach uses its running estimate of the free energy gradient as the adaptive biasing force, eABF is built on the idea that the exact free energy gradient is not necessary for efficient exploration, and that it is still possible to recover the exact free energy separately with an appropriate estimator. eABF does not directly bias the collective coordinates of interest, but rather fictitious variables that are harmonically coupled to them; therefore is does not require second derivative estimates, making it easily applicable to a wider range of problems than ABF. Furthermore, the extended variables present a smoother, coarse-grain-like sampling problem on a mollified free energy surface, leading to faster exploration and convergence. We also introduce CZAR, a simple, unbiased free energy estimator from eABF trajectories. eABF/CZAR converges to the physical free energy surface faster than standard ABF for a wide range of parameters.
A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro.
Trevisani M, Berselli A, Alberini G, Centonze E, Vercellino S, Cartocci V Sci Adv. 2025; 11(2):eadq2616.
PMID: 39792664 PMC: 11721574. DOI: 10.1126/sciadv.adq2616.
Ion and water permeation through claudin-10b and claudin-15 paracellular channels.
Berselli A, Alberini G, Benfenati F, Maragliano L Comput Struct Biotechnol J. 2024; 23:4177-4191.
PMID: 39640531 PMC: 11617971. DOI: 10.1016/j.csbj.2024.11.025.
Isoleucine gate blocks K conduction in C-type inactivation.
Treptow W, Liu Y, Bassetto C, Pinto B, Alves Nunes J, Uriarte R Elife. 2024; 13.
PMID: 39530849 PMC: 11649237. DOI: 10.7554/eLife.97696.
Expanded Functionality and Portability for the Colvars Library.
Fiorin G, Marinelli F, Forrest L, Chen H, Chipot C, Kohlmeyer A J Phys Chem B. 2024; 128(45):11108-11123.
PMID: 39501453 PMC: 11572706. DOI: 10.1021/acs.jpcb.4c05604.
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M J Phys Chem B. 2024; 128(41):9976-10042.
PMID: 39303207 PMC: 11492285. DOI: 10.1021/acs.jpcb.4c04100.