GROMACS: Fast, flexible, and free. - David van der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E. Mark; Herman J. C. Berendsen (J. Comput. Chem., 2005)

Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595. - Lars V. Schäfer; Gerrit Groenhof; Martial Boggio-Pasqua; Michael A. Robb; Helmut Grubmüller (PLoS Comput. Biol., 2008)

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. - Maarten G. Wolf; Martin Hoefling; Camilo Aponte-Santamaría; Helmut Grubmüller; Gerrit Groenhof (J. Comput. Chem., 2010)

Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients. - Maarten G. Wolf; Gerrit Groenhof (J. Comput. Chem., 2012)

Explicit proton transfer in classical molecular dynamics simulations. - Maarten G. Wolf; Gerrit Groenhof (J. Comput. Chem., 2014)

New QM/MM implementation of the DFTB3 method in the gromacs package. - Tomás Kubar; Kai Welke; Gerrit Groenhof (J. Comput. Chem., 2015)

Corrigendum: g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. - Maarten G. Wolf; Martin Hoefling; Camilo Aponte-Santamaría; Helmut Grubmüller; Gerrit Groenhof (J. Comput. Chem., 2016)

GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation. - Bartosz Kohnke; Thomas R. Ullmann; Andreas Beckmann; Ivo Kabadshow; David Haensel; Laura Morgenstern; Plamen Dobrev; Gerrit Groenhof; Carsten Kutzner; Berk Hess; Holger Dachsel; Helmut Grubmüller (Software for Exascale Computing, 2020)

phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. - Anton Jansen; Noora Aho; Gerrit Groenhof; Pavel Buslaev; Berk Hess (J. Chem. Inf. Model., 2024)

Discovery of a Noncompetitive Open-Flap Selective Inhibitor of Plasmepsin II with Antiplasmodial Activity. - Pedro A. Valiente; Yasel Guerra; Maarten G. Wolf; Isel Pascual; Enrique Rudiño-Piñera; Isabelle Florent; Tirso Pons; Gerrit Groenhof (J. Chem. Inf. Model., 2025)