Helmut Grubmüller

35 papers Journal 31Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. J. Comput. Chem. Carsten Kutzner, Vedran Miletic, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L. de Groot, Helmut Grubmüller
2024	J	`jnl`	Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications. CoRR Eliane Briand, Bartosz Kohnke, Carsten Kutzner, Helmut Grubmüller
2024	J	`jnl`	Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation. CoRR Bartosz Kohnke, Eliane Briand, Carsten Kutzner, Helmut Grubmüller
2023	J	`jnl`	Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO J. Chem. Inf. Model. Aharon Gomez, Tobias J. Erb, Helmut Grubmüller, Esteban Vöhringer-Martinez
2022	J	`jnl`	GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. J. Chem. Inf. Model. Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys
2022	J	`jnl`	GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. CoRR Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys
2021	J	`jnl`	A CUDA fast multipole method with highly efficient M2L far field evaluation. Int. J. High Perform. Comput. Appl. Bartosz Kohnke, Carsten Kutzner, Andreas Beckmann, Gert Lube, Ivo Kabadshow, Holger Dachsel, Helmut Grubmüller
2021	J	`jnl`	GROMACS implementation of free energy calculations with non-pairwise Variationally derived Intermediates. Comput. Phys. Commun. Martin Reinhardt, Helmut Grubmüller
2021	J	`jnl`	Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package. Comput. Phys. Commun. Gabor Nagy, Helmut Grubmüller
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`	Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Comput. Biol. Maxim Igaev, Helmut Grubmüller
2019	J	`jnl`	More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018. CoRR Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2019	J	`jnl`	More bang for your buck: Improved use of GPU nodes for GROMACS 2018. J. Comput. Chem. Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2019	J	`jnl`	Sharing Data from Molecular Simulations. J. Chem. Inf. Model. Mark James Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M. J. J. Bonvin, Matthieu Chavent, John D. Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov
2016	J	`jnl`	BASDet: Bayesian approach(es) for structure determination from single molecule X-ray diffraction images. Comput. Phys. Commun. Michal Walczak, Helmut Grubmüller
2016	J	`jnl`	Corrigendum: g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J. Comput. Chem. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof
2016	J	`jnl`	NuSol - Numerical solver for the 3D stationary nuclear Schrödinger equation. Comput. Phys. Commun. Timo Graen, Helmut Grubmüller
2015	J	`jnl`	Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. CoRR Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2015	J	`jnl`	Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comput. Chem. Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2015	J	`jnl`	do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations. Bioinform. Rajendra Kumar, Helmut Grubmüller
2013	J	`jnl`	In silico FRET from simulated dye dynamics. Comput. Phys. Commun. Martin Hoefling, Helmut Grubmüller
2013	—	`conf`	Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. PARCO Carsten Kutzner, Rossen Apostolov, Berk Hess, Helmut Grubmüller
2013	J	`jnl`	g_contacts: Fast contact search in bio-molecular ensemble data. Comput. Phys. Commun. Christian Blau, Helmut Grubmüller
2012	J	`jnl`	Linear-scaling soft-core scheme for alchemical free energy calculations. J. Comput. Chem. Floris P. Buelens, Helmut Grubmüller
2011	J	`jnl`	Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. J. Comput. Chem. Djurre H. De Jong, Lars V. Schäfer, Alex H. de Vries, Siewert J. Marrink, Herman J. C. Berendsen, Helmut Grubmüller
2010	J	`jnl`	g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J. Comput. Chem. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof
2009	J	`jnl`	Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J. Comput. Chem. Maik Goette, Helmut Grubmüller
2009	J	`jnl`	g_permute: Permutation-reduced phase space density compaction. Comput. Phys. Commun. Friedemann Reinhard, Oliver F. Lange, Jochen S. Hub, Jürgen Haas, Helmut Grubmüller
2008	J	`jnl`	Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595. PLoS Comput. Biol. Lars V. Schäfer, Gerrit Groenhof, Martial Boggio-Pasqua, Michael A. Robb, Helmut Grubmüller
2008	J	`jnl`	Polar or Apolar - The Role of Polarity for Urea-Induced Protein Denaturation. PLoS Comput. Biol. Martin C. Stumpe, Helmut Grubmüller
2007	J	`jnl`	Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
2006	J	`jnl`	Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics. J. Comput. Chem. Oliver F. Lange, Lars V. Schäfer, Helmut Grubmüller
2006	—	`conf`	Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
1999	—	`ch.`	Conformational Dynamics Simulations of Proteins. Computational Molecular Dynamics Markus Eichinger, Berthold Heymann, Helmut Heller, Helmut Grubmüller, Paul Tavan
1998	J	`jnl`	Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they? J. Comput. Chem. Helmut Grubmüller, Paul Tavan