Carsten Kutzner
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Explore the profile of Carsten Kutzner including associated specialties, affiliations and a list of published articles.
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14
Citations
4663
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Recent Articles
1.
Kutzner C, Miletic V, Palacio Rodriguez K, Rampp M, Hummer G, de Groot B, et al.
J Comput Chem
. 2025 Feb;
46(5):e70059.
PMID: 39945385
We benchmarked the performance of the GROMACS 2024 molecular dynamics (MD) code on a modern high-performance computing (HPC) cluster with AMD CPUs on up to 65,536 CPU cores. We used...
2.
Kohnke B, Briand E, Kutzner C, Grubmuller H
J Chem Theory Comput
. 2025 Feb;
21(4):1787-1804.
PMID: 39919130
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....
3.
Briand E, Kohnke B, Kutzner C, Grubmuller H
J Chem Theory Comput
. 2025 Feb;
21(4):1762-1786.
PMID: 39919102
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...
4.
Kutzner C, Kniep C, Cherian A, Nordstrom L, Grubmuller H, de Groot B, et al.
J Chem Inf Model
. 2022 Mar;
62(7):1691-1711.
PMID: 35353508
We assess costs and efficiency of state-of-the-art high-performance cloud computing and compare the results to traditional on-premises compute clusters. Our use case is atomistic simulations carried out with the GROMACS...
5.
Kohnke B, Kutzner C, Grubmuller H
J Chem Theory Comput
. 2020 Oct;
16(11):6938-6949.
PMID: 33084336
An important and computationally demanding part of molecular dynamics simulations is the calculation of long-range electrostatic interactions. Today, the prevalent method to compute these interactions is particle mesh Ewald (PME)....
6.
Kutzner C, Pall S, Fechner M, Esztermann A, de Groot B, Grubmuller H
J Comput Chem
. 2019 Jul;
40(27):2418-2431.
PMID: 31260119
We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a...
7.
Igaev M, Kutzner C, Bock L, Vaiana A, Grubmuller H
Elife
. 2019 Mar;
8.
PMID: 30829573
We present a correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to subnanometer. It utilizes a chemically...
8.
GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations
Briones R, Blau C, Kutzner C, de Groot B, Aponte-Santamaria C
Biophys J
. 2018 Dec;
116(1):4-11.
PMID: 30558883
We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics simulations. GROmaρs efficiently computes density maps by fast multi-Gaussian spreading of atomic densities...
9.
Kutzner C, Kopfer D, Machtens J, de Groot B, Song C, Zachariae U
Biochim Biophys Acta
. 2016 Feb;
1858(7 Pt B):1741-52.
PMID: 26874204
Ion channels are of universal importance for all cell types and play key roles in cellular physiology and pathology. Increased insight into their functional mechanisms is crucial to enable drug...
10.
Hess B, Kutzner C, van der Spoel D, Lindahl E
J Chem Theory Comput
. 2015 Dec;
4(3):435-47.
PMID: 26620784
Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS...