Berk Hess - researchr alias

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Viewing Publication 1 - 13 from 13

2024

phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACSAnton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess. jcisd, 64(3):567-574, 2024. [doi]

2020

GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular SimulationBartosz Kohnke, Thomas R. Ullmann, Andreas Beckmann, Ivo Kabadshow, David Haensel, Laura Morgenstern, Plamen Dobrev, Gerrit Groenhof, Carsten Kutzner, Berk Hess, Holger Dachsel, Helmut Grubmüller. In Hans-Joachim Bungartz, Severin Reiz, Benjamin Uekermann, Philipp Neumann, Wolfgang E. Nagel, editors, Software for Exascale Computing - SPPEXA 2016-2019. Volume 136 of Lecture Notes in Computational Science and Engineering, pages 517-543, Springer, 2020. [doi]

2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systemsArne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist. ploscb, 15(1), 2019. [doi]

2017

Sequence dependency of canonical base pair opening in the DNA double helixViveca Lindahl, Alessandra Villa, Berk Hess. ploscb, 13(4), 2017. [doi]

2014

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACSSzilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl. easc 2015: 3-27 [doi]

2013

2011

Copernicus: a new paradigm for parallel adaptive molecular dynamicsSander 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: 60 [doi]

Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architecturesSzilárd Páll, Berk Hess, Erik Lindahl. sc 2011: 71-72 [doi]

2005

GROMACS: Fast, flexible, and freeDavid van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen. jcc, 26(16):1701-1718, 2005. [doi]

1999

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systemsK. Anton Feenstra, Berk Hess, Herman J. C. Berendsen. jcc, 20(8):786-798, 1999. [doi]

1997

LINCS: A linear constraint solver for molecular simulationsBerk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije. jcc, 18(12):1463-1472, 1997. [doi]

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