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2020 – today
- 2024
[j8]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): 567-574 (2024)- 2020
- [p1]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:
GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation. Software for Exascale Computing 2020: 517-543 - [i2]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 abs/2006.09167 (2020)
2010 – 2019
- 2019
- [j7]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) - 2017
- [j6]Viveca Lindahl, Alessandra Villa, Berk Hess:
Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput. Biol. 13(4) (2017) - 2015
- [i1]Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl:
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. CoRR abs/1506.00716 (2015) - 2014
- [c4]Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl:
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. EASC 2014: 3-27 - 2013
- [j5]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): 845-854 (2013) - [j4]Szilárd Páll, Berk Hess:
A flexible algorithm for calculating pair interactions on SIMD architectures. Comput. Phys. Commun. 184(12): 2641-2650 (2013) - [c3]Carsten Kutzner, Rossen Apostolov, Berk Hess, Helmut Grubmüller:
Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. PARCO 2013: 722-727 - 2011
- [c2]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: 60:1-60:10 - [c1]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: 71-72
2000 – 2009
- 2005
- [j3]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): 1701-1718 (2005)
1990 – 1999
- 1999
- [j2]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): 786-798 (1999) - 1997
- [j1]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): 1463-1472 (1997)
Coauthor Index
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