Herman J. C. Berendsen - researchr alias

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Viewing Publication 1 - 13 from 13

2013

MPI Parallelization of Innovative DPD ThermostatsNicolae Goga, Herman J. C. Berendsen, Svetlana Baoukina, S. A. Moga, G. Dragoi, A. Hadar, B. Paviloiu. ichi 2013: 476 [doi]

2011

Determining equilibrium constants for dimerization reactions from molecular dynamics simulationsDjurre H. De Jong, Lars V. Schäfer, Alex H. De Vries, Siewert J. Marrink, Herman J. C. Berendsen, Helmut Grubmüller. jcc, 32(9):1919-1928, 2011. [doi]

2005

GROMACS: Fast, flexible, and freeDavid van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen. jcc, 26(16):1701-1718, 2005. [doi]

1999

Molecular Dynamics Simulations: The Limits and BeyondHerman J. C. Berendsen. In Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas. Volume 4 of Lecture Notes in Computational Science and Engineering, pages 3-36, Springer, 1999. [doi]

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systemsK. Anton Feenstra, Berk Hess, Herman J. C. Berendsen. jcc, 20(8):786-798, 1999. [doi]

Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic esterMarc F. Lensink, Janez Mavri, Herman J. C. Berendsen. jcc, 20(8):886-895, 1999. [doi]

1997

LINCS: A linear constraint solver for molecular simulationsBerk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije. jcc, 18(12):1463-1472, 1997. [doi]

A comparison of techniques for calculating protein essential dynamicsDaan M. F. van Aalten, Bert L. de Groot, John B. C. Findlay, Herman J. C. Berendsen, Andrea Amadei. jcc, 18(2):169-181, 1997. [doi]

1996

Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integratorMarc F. Lensink, Janez Mavri, Herman J. C. Berendsen. jcc, 17(11):1287-1295, 1996. [doi]

The Amfisbaena: A Parallel Sup computer System Based on i860 as a Generic Platform for Molecular Dynamics SimulationRudi van Drunen, Cees van Teylingen, Marcel Kroontje, Herman J. C. Berendsen. pdpta 1996: 637-644

1992

Conformational search by potential energy annealing: Algorithm and application to cyclosporin ARené C. van Schaik, Wilfred F. van Gunsteren, Herman J. C. Berendsen. jcamd, 6(2):97-112, 1992.

1988

Dynamic simulation as an essential tool in molecular modelingHerman J. C. Berendsen. jcamd, 2(3):217-221, 1988. [doi]

1987

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistryWilfred F. van Gunsteren, Herman J. C. Berendsen. jcamd, 1(2):171-176, 1987. [doi]

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