Výsledky vyhledávání - "Kutzner Carsten"

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Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation

Autor: Kohnke, Bartosz, Briand, Eliane, Kutzner, Carsten, Grubmüller, Helmut

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn, conformationa

Externí odkaz: http://arxiv.org/abs/2410.01754

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Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications

Autor: Briand, Eliane, Kohnke, Bartosz, Kutzner, Carsten, Grubmüller, Helmut

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversel

Externí odkaz: http://arxiv.org/abs/2410.01626

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GROMACS in the cloud: A global supercomputer to speed up alchemical drug design

Autor: Kutzner, Carsten, Kniep, Christian, Cherian, Austin, Nordstrom, Ludvig, Grubmüller, Helmut, de Groot, Bert L., Gapsys, Vytautas

Publikováno v: Journal of Chemical Information and Modelling, 2022, 62, 1691-1711

We assess costs and efficiency of state-of-the-art high performance cloud computing compared to a traditional on-premises compute cluster. Our use case are atomistic simulations carried out with the GROMACS molecular dynamics (MD) toolkit with a focu

Externí odkaz: http://arxiv.org/abs/2201.06372

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More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018

Autor: Kutzner, Carsten, Páll, Szilárd, Fechner, Martin, Esztermann, Ansgar, de Groot, Bert L., Grubmüller, Helmut

Publikováno v: Journal of Computational Chemistry, 2019, 40, 2418-2431

We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the

Externí odkaz: http://arxiv.org/abs/1903.05918

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Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

Autor: Kutzner, Carsten, Páll, Szilárd, Fechner, Martin, Esztermann, Ansgar, de Groot, Bert L., Grubmüller, Helmut

Publikováno v: Journal of Computational Chemistry, 2015, 36, 1990-2008

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD, multi-threading, and

Externí odkaz: http://arxiv.org/abs/1507.00898

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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

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

Publikováno v: Proc. EASC 2014, 8759 pp. 3-27, Springer LNCS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in

Externí odkaz: http://arxiv.org/abs/1506.00716

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