GROMACS: Fast, flexible, and free von Van Der Spoel, David, Lindahl, Erik, Hess, Berk, Groenhof, Gerrit, Mark, Alan E., Berendsen, Herman J. C.

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High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating von Melo, Manuel N, Arnarez, Clément, Sikkema, Hendrik, Kumar, Neeraj, Walko, Martin, Berendsen, Herman J. C, Kocer, Armagan, Marrink, Siewert J, Ingólfsson, Helgi I

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Photoactivation of the Photoactive Yellow Protein:  Why Photon Absorption Triggers a Trans-to-Cis Isomerization of the Chromophore in the Protein von Groenhof, Gerrit, Bouxin-Cademartory, Mathieu, Hess, Berk, de Visser, Sam P., Berendsen, Herman J. C., Olivucci, Massimo, Mark, Alan E., Robb, Michael A.

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Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems von Feenstra, K. Anton, Hess, Berk, Berendsen, Herman J. C.

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Determining equilibrium constants for dimerization reactions from molecular dynamics simulations von De Jong, Djurre H., Schäfer, Lars V., De Vries, Alex H., Marrink, Siewert J., Berendsen, Herman J. C., Grubmüller, Helmut

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LINCS: A linear constraint solver for molecular simulations von Hess, Berk, Bekker, Henk, Berendsen, Herman J. C., Fraaije, Johannes G. E. M.

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Computer Simulation of Urea−Water Mixtures:  A Test of Force Field Parameters for Use in Biomolecular Simulation von Smith, Lorna J, Berendsen, Herman J. C, van Gunsteren, Wilfred F

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Molecular dynamics simulations as a tool for improving protein stability von Pikkemaat, Mariël G., Linssen, Antonius B.M., Berendsen, Herman J.C., Janssen, Dick B.

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A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field von van der Spoel, David, van Maaren, Paul J., Berendsen, Herman J. C.

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Dynamic Conformations of Flavin Adenine Dinucleotide:  Simulated Molecular Dynamics of the Flavin Cofactor Related to the Time-Resolved Fluorescence Characteristics von van den Berg, Petra A. W, Feenstra, K. Anton, Mark, Alan E, Berendsen, Herman J. C, Visser, Antonie J. W. G

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Wilfred van Gunsteren: 35 Years of Biomolecular Simulation von Hünenberger, Philippe H, Mark, Alan E, Berendsen, Herman J.C

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Calculation of the Redox Potential of the Protein Azurin and Some Mutants von van den Bosch, Marieke, Swart, Marcel, Snijders†, Jaap G, Berendsen, Herman J.C, Mark, Alan E, Oostenbrink, Chris, van Gunsteren, Wilfred F, Canters, Gerard W

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An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge de... von Saint-Martin, Humberto, Hess, Berk, Berendsen, Herman J C

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Essential dynamics of proteins von Amadei, Andrea, Linssen, Antonius B. M., Berendsen, Herman J. C.

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Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme von Hayward, Steven, Berendsen, Herman J.C.

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Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry von van Gunsteren, Wilfred F., Berendsen, Herman J. C.

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Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore von Groenhof, Gerrit, Lensink, Marc F., Berendsen, Herman J. C., Snijders, Jaap G., Mark, Alan E.

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A mobile charge densities in harmonic oscillators (MCDHO) molecular model for numerical simulations: The water–water interaction von Saint-Martin, Humberto, Hernández-Cobos, Jorge, Bernal-Uruchurtu, Margarita I., Ortega-Blake, Iván, Berendsen, Herman J. C.

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An Alamethicin Channel in a Lipid Bilayer: Molecular Dynamics Simulations von Peter Tieleman, D., Berendsen, Herman J.C., Sansom, Mark S.P.

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Lipid Properties and the Orientation of Aromatic Residues in OmpF, Influenza M2, and Alamethicin Systems:  Molecular Dynamics Simulations von Tieleman, D. Peter, Forrest, Lucy R, Sansom, Mark S. P, Berendsen, Herman J. C

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