Jérôme Hénin
University of Paris
48 Papers
104 Citations
Jérôme Hénin is an academic researcher from University of Paris. The author has contributed to research in topics: Chemistry & Molecular dynamics. The author has an hindex of 25, co-authored 44 publications. Previous affiliations of Jérôme Hénin include National Institute of Advanced Industrial Science and Technology & PSL Research University.
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Papers
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C. Phillips,David J. Hardy,Julio D.C. Maia,John E. Stone,João V. Ribeiro,Rafael C. Bernardi,Ronak Buch,Giacomo Fiorin,Jérôme Hénin,Wei Jiang,Ryan McGreevy,Marcelo C. R. Melo,Brian K. Radak,Robert D. Skeel,Abhishek Singharoy,Yi Wang,Benoît Roux,Aleksei Aksimentiev,Zaida Luthey-Schulten,Laxmikant V. Kale,Klaus Schulten,Christophe Chipot,Emad Tajkhorshid +22 more
TL;DR: The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
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Using collective variables to drive molecular dynamics simulations
TL;DR: The modular framework presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods, and is extensible, and portable between commonly used MD simulation engines.
960
Overcoming free energy barriers using unconstrained molecular dynamics simulations
Jérôme Hénin,Christophe Chipot +1 more
TL;DR: Association of unconstrained molecular dynamics and the formalisms of thermodynamic integration and average force and the illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method.
498
The adaptive biasing force method: everything you always wanted to know but were afraid to ask.
Jeffrey Comer,James C. Gumbart,Jérôme Hénin,Tony Lelièvre,Andrew Pohorille,Andrew Pohorille,Christophe Chipot +6 more
TL;DR: In this contribution, the adaptive biasing force algorithm is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability, and inherent limitations, as well as introducing novel extensions.
464
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
TL;DR: Numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube, and similarities and differences between the ABF and metadynamics schemes are discussed.
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