@article {2021|2149,
	title = {Fast and Accurate Multidimensional Free Energy Integration.},
	journal = {J Chem Theory Comput},
	volume = {17},
	year = {2021},
	month = {2021 Nov 09},
	pages = {6789-6798},
	abstract = {<p>Enhanced sampling and free energy calculation algorithms of the thermodynamic integration family (such as the adaptive biasing force (ABF) method) are not based on the direct computation of a free energy surface but rather of its gradient. Integrating the free energy surface is nontrivial in dimensions higher than one. Here, the author introduces a flexible, portable implementation of a Poisson equation formalism to integrate free energy surfaces from estimated gradients in dimensions 2 and 3 using any combination of periodic and nonperiodic (Neumann) boundary conditions. The algorithm is implemented in portable C++ and provided as a standalone tool that can be used to integrate multidimensional gradient fields estimated on a grid using any algorithm, such as umbrella integration as a post-treatment of umbrella sampling simulations. It is also included in the implementation of ABF (and its extended-system variant eABF) in the Collective Variables Module, enabling the seamless computation of multidimensional free energy surfaces within ABF and eABF simulations. A Python-based analysis toolchain is provided to easily plot and analyze multidimensional ABF simulation results, including metrics to assess their convergence. The Poisson integration algorithm can also be used to perform Helmholtz decomposition of noisy gradient estimates on the fly, resulting in an efficient implementation of the projected ABF (pABF) method proposed by Leli{\'e}vre and co-workers. In numerical tests, pABF is found to lead to faster convergence with respect to ABF in simple cases of low intrinsic dimension but seems detrimental to convergence in a more realistic case involving degenerate coordinates and hidden barriers due to slower exploration. This suggests that variance reduction schemes do not always yield convergence improvements when applied to enhanced sampling methods.</p>
},
	issn = {1549-9626},
	doi = {10.1021/acs.jctc.1c00593},
	author = {J{\'e}r{\^o}me H{\'e}nin}
}
@inbook {2014|1720,
	title = {Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins},
	booktitle = {Membrane Proteins Production for Structural Analysis},
	year = {2014},
	pages = {347{\textendash}392},
	publisher = {Springer New York},
	organization = {Springer New York},
	author = {J{\'e}r{\^o}me H{\'e}nin and Marc Baaden and Antoine Taly}
}
