Heymann, B.; Grubmueller, H.: Molecular dynamics force probe simulations of antibody/antigen unbinding: Entropic control and non-additivity of unbinding forces. Biophysical Journal 81 (3), pp. 1295 - 1313 (2001)

Rief, M.; Grubmueller, H.: Kraftspektroskopie von einzelnen Biomolekülen. Physikalische Blätter 2, pp. 55 - 61 (2001)

Heymann, J. B.; Pfeiffer, M.; Hildebrandt, V.; Kaback, H. R.; Fotiadis, D.; de Groot, B. L.; Engel, A.; Oesterhelt, D.; Müller, D. J.: Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Structure with Folding and Design 8 (6), pp. 643 - 653 (2000)

de Groot, B. L.; Heymann, B.; Engel, A.; Mitsuoka, K.; Fujiyoshi, Y.; Grubmueller, H.: The fold of human Aquaporin 1. Journal of Molecular Biology 300, pp. 987 - 994 (2000)

Heymann, B.; Grubmueller, H.: Dynamic force spectroscopy of molecular adhesion bonds. Physical Review Letters 84, pp. 6126 - 6129 (2000)

Ossig, R.; Schmitt, H. D.; de Groot, B. L.; Riedel, D.; Keraenen, S.; Ronne, H.; Grubmueller, H.; Jahn, R.: Exocytosis requires asymmetry in the central layer of the SNARE complex. EMBO Journal 19, pp. 6000 - 6010 (2000)

Schulze, B.; Grubmueller, H.; Evanseck, J. D.: Functional significance of hierarchical tiers in carbonmonoxy myoglobin: Conformational substates and transitions studied by conformational flooding simulations. Journal of the American Chemical Society 122, pp. 8700 - 8711 (2000)

Stahlberg, H.; Braun, T.; de Groot, B. L.; Philippsen, A.; Borgnia, M. J.; Agre, P.; Kuehlbrandt, W.; Engel, A.: The 6.9Å Structure of GlpF: A Basis for Homology Modeling of the Glycerol Channel from Escherichia coli. Journal of Structural Biology 132, pp. 133 - 141 (2000)

de Groot, B. L.; Vriend, G.; Berendsen, H. J. C.: Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism. Journal of Molecular Biology 286 (4), pp. 1241 - 1249 (1999)

Grubmüller, H.; Heymann, B.: Proteindynamik von Ligand/Rezeptor-Bindungen. MPIbpc News 1, pp. 1 - 4 (1999)

Heymann, B.; Grubmueller, H.: AN02/DNP-hapten unbinding forces studied by molecular dynamics atomic force microscopy simulations. Chemical Physics Letters 303, pp. 1 - 9 (1999)

Heymann, B.; Grubmueller, H.: ’Chair-boat‘ transitions and side groups affect the stiffness of polysaccharides. Chemical Physics Letters 305, pp. 202 - 208 (1999)

Heymann, B.; Grubmüller, H.: Elastic properties of poly(ethylene-glycol) studied by molecular dynamics stretching simulations. Chemical Physics Letters 307, pp. 425 - 432 (1999)

van Aalten, D. M. F.; de Groot, B. L.; Berendsen, H. J. C.; Findlay, J. B. C.; Amadei, A.: A comparison of techniques for calculating protein essential dynamics. Journal of Computational Chemistry 18 (2), pp. 169 - 181 (1998)

Grubmüller, H.; Tavan, P.: Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they? Journal of computational chemistry 19 (13), pp. 1534 - 1552 (1998)

Eichinger, M.; Grubmüller, H.; Heller, H.; Tavan, P.: FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. Journal of Computational Chemistry 18 (14), pp. 1729 - 1749 (1997)

Grubmüller, H.; Heymann, B.; Tavan, P.: Simulation eines molekularen Erkennungsvorgangs. Spektrum der Wissenschaft 1997 (3), pp. 14 - 16 (1997)

Grubmüller, H.; Heymann, B.; Tavan, P.: Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force. Science (5251), pp. 997 - 999 (1996)

Grubmüller, H.: Predicting slow structural transitions in macromolecular systems: Conformational flooding. Physical Review E 52 (3), pp. 2893 - 2906 (1995)

Grubmüller, H.; Tavan, P.: Molecular dynamics of conformational substates for a simplified protein model. Journal of Chemical Physics 101 (6), pp. 5047 - 5057 (1994)

Grubmüller, H.; Döhring, K.; Tavan, P.; Nonella, M.; Oesterhelt, D.: BR at work: a computeranimation for the 13-14-cis-model of the photochemical cycle of bacteriorhodopsin. Journal of molecular graphics 11 (4), p. 258 (1993)

Grubmüller, H.; Heller, H.; Windemuth, A.; Schulten, K.: Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Molecular Simulation 6 (1-3), pp. 121 - 142 (1991)

Heller, H.; Grubmüller, H.; Schulten, K.: Molecular dynamics simulation on a parallel computer. Molecular simulation 5 (3-4), pp. 133 - 165 (1990)

Tavan, P.; Grubmüller, H.; Kühnel, H.: Self-organization of associative memory and pattern classification: recurrent signal processing on topological feature maps. Biological cybernetics 64 (2), pp. 95 - 105 (1990)

Grubmüller, H.; Heller, H.; Schulten, K.: Eine CRAY für "jedermann". mc Die Microcomputer-Zeitschrift (11), pp. 48 - 65 (1988)

Eichinger, M.; Heller, H.; Grubmueller, H.: EGO - An efficient molecular dynamics program and its application to protein dynamics simulations. World Scientific, Singapore (1999)

Moffat, M.; Changeux, J. P.; Crothers, D. M.; Grubmueller, H.; Nienhaus, G. U.; Palma, M. U.; Parak, F. G.; Schulten, K.; Warshel, A.: How does complexity lead to apparently simple function? Dahlem University Press, Berlin (1999)

Eichinger, M.; Heymann, B.; Heller, H.; Grubmueller, H.; Tavan, P.: Conformational dynamics simulations of proteins. Springer, Berlin (1998)

Bebon, R.; Godec, A.: Concentration of Empirical First-Passage Times. In: Target Search Problems, pp. 31 - 53 (Eds. Grebenkov, D.; Metzler, R.; Oshanin, G.). Springer Nature Switzerland, Cham (2024)

von Ardenne, B.; Grubmüller, H.: Single Particle Imaging with FEL Using Photon Correlations. In: Nanoscale Photonic Imaging, pp. 435 - 455 (Eds. Salditt, T.; Egner, A.; Luke, D. R.). Springer, Cham (2020)

Kohnke, B.; Ullmann, R. T.; Beckman, A.; Kabadshow, I.; Haensel, D.; Morgenstern, L.; Dobrev, P.; Groenhof, G.; Kutzner, C.; Hess, B. et al.; Dachsel, H.; Grubmüller, H.: GROMEX: A scalable and versatile fast multipole method for biomolecular simulation. In: Software for Exascale Computing - SPPEXA 2016-2019, pp. 517 - 543 (Eds. Bungartz, H.-J.; Reiz, S.; Uekermann, B.; Neumann, P.; Nagel, W. E.). Springer, Cham (2020)

von Ardenne, B.; Grubmüller, H.: Single particle imaging with FEL using photon correlations. In: Nanoscale Photonic Imaging, pp. 435 - 455 (Eds. Salditt, T.; Egner, A.; Luke, D.). Springer, Cham (2020)

Aldeghi, M.; de Groot, B. L.; Gapsys, V.: Accurate calculation of free energy changes upon amino acid mutation. In: Computational Methods in Protein Evolution, pp. 19 - 47 (Ed. Sikosek, T.). Springer Nature, New York (2019)

Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From protein structure to function with bioinformatics, pp. 393 - 425 (Ed. Rigden, D. J.). Springer, Dordrecht (2017)

Gapsys, V.; Michielssens, S.; Peters, J. H.; de Groot, B.; Leonov, H.: Calculation of binding free energies. In: Molecular Modeling of Proteins, pp. 173 - 209 (Ed. Kukol, A.). Humana Pr.; Springer, New York, N.Y. (2015)

Páll, S.; Abraham, M. J.; Kutzner, C.; Hess, B.; Lindahl, E.: Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In: Solving Software Challenges for Exascale: International Conference on Exascale Applications and Software, EASC 2014, Stockholm, Sweden, April 2-3, 2014, Revised Selected Papers, pp. 3 - 27 (Eds. Markidis, S.; Laure, E.). Springer, Cham (2015)

Kutzner, C.; Apostolov, R.; Hess, B.; Grubmüller, H.: Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. In: Parallel Computing: Accelerating Computational Science and Engineering (CSE), pp. 722 - 730 (Eds. Bader, M.; Bode, A.; Bungartz, H. J.). IOS Press, Amsterdam (2014)

Groenhof, G.: Introduction to QM/MM simulations. In: Biomolecular Simulations: Mehods and Protocols, pp. 43 - 66 (Eds. Monticelli, L.; Salonen, E.). Humana Pr.; Springer, New York (2013)

Groenhof, G.; Boggio-Pasqua, M.; Schäfer, L. V.; Robb, M. A.: Computer simulations of photobiological processes: The effect of the protein environment. In: Combining quantum mechanics and molecular mechanics. Some recent progresses in QM/MM methods, pp. 181 - 212 (Eds. Sabin, J. R.; Braendas, E.; Canuto, S.). Elsevier, Amsterdam (2010)

Groenhof, G.; Schaefer, L. V.; Boggio-Pasqua, M.; Robb, M. A.: Excited state dynamics in biomolecules. In: Handbook of molecular biophysics, pp. 93 - 128 (Ed. Bohr, H. G.). Wiley-VCH, Weinheim (2009)

Hub, J.; Grubmuller, H.; de Groot, B. L.: Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? In: Aquaporins, pp. 57 - 76 (Ed. Beitz, E.). Springer, Berlin (2009)

Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From Protein Structure to Function with Bioinformatics, pp. 217 - 249 (Ed. Rigden, D.J.). Springer, Dordrecht (2009)

Hayward, S.; de Groot, B. L.: Normal modes and essential dynamics. In: Molecular modeling of proteins, pp. 89 - 106 (Ed. Kukol, A.). Humana Pr., Totowa, N. Y. (2008)

Grubmueller, H.; Seeger, S.; Tschesche, H.: Aufbau, Funktion und Diagnostik biogener Moleküle. In: Gase, Nanosysteme, Flüssigkeiten, pp. 977 - 1067 (Ed. Kleinermanns, K.). de Gruyter, Berlin (2006)

Kutzner, C.; van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; de Groot, B. L.; Grubmueller, H.: Improved GROMACS scaling on ethernet switched clusters. In: Recent advances in parallel virtual machine and message passing interface. 13th European PVM/MPI User`s Group meeting, Bonn, Germany, September 17-20, 2006, pp. 404 - 405 (Eds. Mohr, B.; Larsson, T. J.; Worringen, J.; Dongarra, J.). Springer, Berlin (2006)

Grubmueller, H.: Force probe molecular dynamics simulations. In: Protein-ligand interactions; methods and applications, pp. 493 - 515 (Ed. Nienhaus, U.). Humana Pr., Totowa, NJ. (2005)

Grubmueller, H.: Proteins as molecular machines: force probe simulations. In: Computational soft matter: From synthetic polymers to proteins; Winter School, 29. Febr. - 6. March, 2004, Gustav-Stresemann-Institut Bonn, pp. 401 - 421 (Eds. Attig, N.; Binder, K.; Grubmueller, H.; Kremer, K.). John von Neumann Institute for Computing, Jülich (2004)

Tavan, P.; Grubmüller, H.: Selbstorganisation von Assoziativspeichern und Musterklassifikatoren: Rekurrente Signalverarbeitung auf topologischen Merkmalskarten. In: Kleinheubacher Berichte, Vol. 34, pp. 573 - 582 (1991)

Hui, C.; de Vries, R.; Kopec, W.; de Groot, B. L.: Effective Polarization in Potassium Channel Simulations: Ion Conductance, Occupancy, Voltage Response, and Selectivity. bioRxiv (2025)

Wilson, C. J.; Gapsys, V.; de Groot, B. L.: Improving pKa prediction accuracy with reparametrized force fields and free energy calculations. ChemRxiv (2025)

Kalutskii, M.; Grubmüller, H.; Volkov, V. A.; Igaev, M.: Microtubule dynamics are defined by conformations and stability of clustered protofilaments. bioRxiv (2024)

Otteson, L.; Nagy, G.; Kunkel, J.; Kodis, G.; Zheng, W.; Bignon, C.; Longhi, S.; Grubmüller, H.; Vaiana, A. C.; Vaiana, S. M.: Transient Non-local Interactions Dominate the Dynamics of Measles Virus N_TAIL. bioRxiv (2024)

Griesinger, C.; Sant, V.; Matthes, D.; Mazal, H.; Antonschmidt, L.; Wieser, F.; Tekwani Movellan, K.; Xue, K.; Nimerovsky, E.; Stampolaki, M. et al.; Nathan, M.; Riedel, D.; Becker, S.; Sandoghdar, V.; de Groot, B. L.; Andreas, L. B.: Lipidic folding pathway of α-Synuclein via a toxic oligomer. Research Square (2024)

Luke, D. R.; Schultze, S.; Grubmüller, H.: Stochastic Algorithms for Large-Scale Composite Optimization: the Case of Single-Shot X-FEL Imaging. arXiv (2024)

Vossel, M.; de Groot, B. L.; Godec, A.: The allosteric lever: towards a principle of specific allosteric response. arXiv (2023)

Eltzner, B.; Hofstadler, J.; Rudolf, D.; Habeck, M.; de Groot, B. L.: Bayesian Maximum Entropy Ensemble Refinement. bioRxiv (2023)

Wiechers, H.; Zobel, M.; Bennati, M.; Tkach, I.; Eltzner, B.; Huckemann, S.; Pokern, Y.: Drift Models on Complex Projective Space for Electron-Nuclear Double Resonance. arXiv (2023)

Schultze, S.; Grubmüller, H.: Bayesian structure determination of multiple conformational structures from single-molecule X-ray scattering images. arXiv (2023)

Schultze, S.; Grubmüller, H.: De novo structural ensemble determination from single-molecule X-ray scattering: A Bayesian approach. arXiv (2023)

Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. arXiv (2023)

Blom, K.; Godec, A.: Global Speed Limit for Finite-Time Dynamical Phase Transition and Nonequilibrium Relaxation. arXiv (2022)

Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations. arXiv (2022)

Dieball, C.; Godec, A.: Feynman-Kac theory of time-integrated functionals: Itô versus functional calculus. arXiv (2022)

Hartich, D.; Godec, A.: Violation of Local Detailed Balance Despite a Clear Time-Scale Separation. arXiv (2021)

Nagy, G.; Grubmüller, H.: How accurate are circular dichroism based secondary structure estimates? bioRxiv (2020)