LINCS: A linear constraint solver for molecular simulations. - Berk Hess; Henk Bekker; Herman J. C. Berendsen; Johannes G. E. M. Fraaije (J. Comput. Chem., 1997)

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. - K. Anton Feenstra; Berk Hess; Herman J. C. Berendsen (J. Comput. Chem., 1999)

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)

Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures. - Szilárd Páll; Berk Hess; Erik Lindahl (SC Companion, 2011)

Copernicus: a new paradigm for parallel adaptive molecular dynamics. - Sander Pronk; Per Larsson; Iman Pouya; Gregory R. Bowman; Imran S. Haque; Kyle Beauchamp; Berk Hess; Vijay S. Pande; Peter M. Kasson; Erik Lindahl (SC, 2011)

Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. - Carsten Kutzner; Rossen Apostolov; Berk Hess; Helmut Grubmüller (PARCO, 2013)

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. - Sander Pronk; Szilárd Páll; Roland Schulz; Per Larsson; Pär Bjelkmar; Rossen Apostolov; Michael R. Shirts; Jeremy C. Smith; Peter M. Kasson; David van der Spoel; Berk Hess; Erik Lindahl (Bioinform., 2013)

A flexible algorithm for calculating pair interactions on SIMD architectures. - Szilárd Páll; Berk Hess (Comput. Phys. Commun., 2013)

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. - Szilárd Páll; Mark James Abraham; Carsten Kutzner; Berk Hess; Erik Lindahl (EASC, 2014)

Sequence dependency of canonical base pair opening in the DNA double helix. - Viveca Lindahl; Alessandra Villa; Berk Hess (PLoS Comput. Biol., 2017)

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. - Arne Elofsson; Berk Hess; Erik Lindahl; Alexey Onufriev; David van der Spoel; Anders Wallqvist (PLoS Comput. Biol., 2019)

Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. - Szilárd Páll; Artem A. Zhmurov; Paul Bauer; Mark James Abraham; Magnus Lundborg; Alan Gray; Berk Hess; Erik Lindahl (CoRR, 2020)

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)