Berk Hess

According to our database, Berk Hess authored at least 14 papers between 1997 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

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

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

Proceedings of the Software for Exascale Computing - SPPEXA 2016-2019, 2020

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

2019

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

2017

Sequence dependency of canonical base pair opening in the DNA double helix.

Viveca Lindahl, Alessandra Villa, Berk Hess

PLoS Comput. Biol., 2017

2014

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS.

Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl

Proceedings of the Solving Software Challenges for Exascale, 2014

2013

A flexible algorithm for calculating pair interactions on SIMD architectures.

Szilárd Páll, Berk Hess

Comput. Phys. Commun., 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

Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.

Carsten Kutzner, Rossen Apostolov, Berk Hess, Helmut Grubmüller

Proceedings of the Parallel Computing: Accelerating Computational Science and Engineering (CSE), 2013

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

Proceedings of the Conference on High Performance Computing Networking, 2011

Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures.

Szilárd Páll, Berk Hess, Erik Lindahl

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, 2011

2005

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

1999

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

1997

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