A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. - Vincent Kräutler; Wilfred F. van Gunsteren; Philippe H. Hünenberger (J. Comput. Chem., 2001)

A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions. - Tim N. Heinz; Philippe H. Hünenberger (J. Comput. Chem., 2004)

The GROMOS software for biomolecular simulation: GROMOS05. - Markus Christen; Philippe H. Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P. Geerke; Tim N. Heinz; Mika A. Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; et al. (J. Comput. Chem., 2005)

A new GROMOS force field for hexopyranose-based carbohydrates. - Roberto D. Lins; Philippe H. Hünenberger (J. Comput. Chem., 2005)

An improved nucleic acid parameter set for the GROMOS force field. - Thereza A. Soares; Philippe H. Hünenberger; Mika A. Kastenholz; Vincent Kräutler; Thomas Lenz; Roberto D. Lins; Chris Oostenbrink; Wilfred F. van Gunsteren (J. Comput. Chem., 2005)

A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations. - Vincent Kräutler; Philippe H. Hünenberger (J. Comput. Chem., 2006)

Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water. - Halvor S. Hansen; Philippe H. Hünenberger (J. Comput. Chem., 2010)

A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. - Halvor S. Hansen; Philippe H. Hünenberger (J. Comput. Chem., 2011)

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. - Bruno A. C. Horta; Zhixiong Lin; Wei Huang; Sereina Riniker; Wilfred F. van Gunsteren; Philippe H. Hünenberger (J. Comput. Chem., 2012)

New functionalities in the GROMOS biomolecular simulation software. - Anna-Pitschna E. Kunz; Jane R. Allison; Daan P. Geerke; Bruno A. C. Horta; Philippe H. Hünenberger; Sereina Riniker; Nathan Schmid; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS. - Noah S. Bieler; Philippe H. Hünenberger (J. Comput. Chem., 2015)

Revision of the GROMOS 56A6CARBO force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. - Wojciech Plazinski; Alice Lonardi; Philippe H. Hünenberger (J. Comput. Chem., 2016)

An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. - Gerhard König; Nina Glaser; Benjamin Schroeder 002; Alzbeta Kubincová; Philippe H. Hünenberger; Sereina Riniker (J. Chem. Inf. Model., 2020)

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. - Benjamin Ries; Salomé Rieder; Clemens Rhiner; Philippe H. Hünenberger; Sereina Riniker (J. Comput. Aided Mol. Des., 2022)

Simultaneous parametrization of torsional and third-neighbor interaction terms in force-field development: The LLS-SC algorithm. - Yan M. H. Gonçalves; Sadra Kashefolgheta; Marina P. Oliveira; Philippe H. Hünenberger; Bruno A. C. Horta (J. Comput. Chem., 2022)

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. - Salomé Rieder; Benjamin Ries; Kay Schaller; Candide Champion; Emília P. Barros; Philippe H. Hünenberger; Sereina Riniker (J. Chem. Inf. Model., 2022)

Development of an open-source software for isomer enumeration. - Salomé Rieder; Marina P. Oliveira; Sereina Riniker; Philippe H. Hünenberger (J. Cheminformatics, 2023)