Berk Hess

15 papers A 1Journal 10Unranked 3
YearRankTypeTitle / Venue / Authors
2024 J jnl
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.
J. Chem. Inf. Model.
Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess
2020 — ch.
GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation.
Software for Exascale Computing
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
2020 J jnl
Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS.
CoRR
Szilárd Páll, Artem A. Zhmurov, Paul Bauer, Mark James Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl
2019 J jnl
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.
PLoS Comput. Biol.
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
2017 J jnl
Sequence dependency of canonical base pair opening in the DNA double helix.
PLoS Comput. Biol.
Viveca Lindahl, Alessandra Villa, Berk Hess
2015 J jnl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS.
CoRR
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
2014 — conf
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS.
EASC
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
2013 J jnl
A flexible algorithm for calculating pair interactions on SIMD architectures.
Comput. Phys. Commun.
Szilárd Páll, Berk Hess
2013 J jnl
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Bioinform.
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
2013 — conf
Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.
PARCO
Carsten Kutzner, Rossen Apostolov, Berk Hess, Helmut Grubmüller
2011 A conf
Copernicus: a new paradigm for parallel adaptive molecular dynamics.
SC
Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl
2011 — conf
Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures.
SC Companion
Szilárd Páll, Berk Hess, Erik Lindahl
2005 J jnl
GROMACS: Fast, flexible, and free.
J. Comput. Chem.
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
1999 J jnl
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems.
J. Comput. Chem.
K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen
1997 J jnl
LINCS: A linear constraint solver for molecular simulations.
J. Comput. Chem.
Berk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije