Berk Hess

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 5

Top Topics

Protein Folding

Scientific Computing

Molecular Dynamics Simulations

Top Venues

PLoS Comput. Biol.

J. Chem. Inf. Model.

Publications

Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. J. Chem. Inf. Model. 64 (3) (2024)
Szilárd Páll, Artem A. Zhmurov, Paul Bauer, Mark James Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl
Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. CoRR (2020)
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15 (1) (2019)
Viveca Lindahl, Alessandra Villa, Berk Hess
Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput. Biol. 13 (4) (2017)
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. CoRR (2015)
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. EASC (2014)
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
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 29 (7) (2013)
Carsten Kutzner, Rossen Apostolov, Berk Hess, Helmut Grubmüller
Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. PARCO (2013)
Szilárd Páll, Berk Hess
A flexible algorithm for calculating pair interactions on SIMD architectures. Comput. Phys. Commun. 184 (12) (2013)
Szilárd Páll, Berk Hess, Erik Lindahl
Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures. SC Companion (2011)
Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl
Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC (2011)
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26 (16) (2005)
K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 20 (8) (1999)
Berk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije
LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18 (12) (1997)