Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. - Wilfred F. van Gunsteren; Herman J. C. Berendsen (J. Comput. Aided Mol. Des., 1987)

Dynamic simulation as an essential tool in molecular modeling. - Herman J. C. Berendsen (J. Comput. Aided Mol. Des., 1988)

Conformational search by potential energy annealing: Algorithm and application to cyclosporin A. - René C. van Schaik; Wilfred F. van Gunsteren; Herman J. C. Berendsen (J. Comput. Aided Mol. Des., 1992)

The Amfisbaena: A Parallel Sup computer System Based on i860 as a Generic Platform for Molecular Dynamics Simulation. - Rudi van Drunen; Cees van Teylingen; Marcel Kroontje; Herman J. C. Berendsen (PDPTA, 1996)

Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator. - Marc F. Lensink; Janez Mavri; Herman J. C. Berendsen (J. Comput. Chem., 1996)

A comparison of techniques for calculating protein essential dynamics. - Daan M. F. van Aalten; Bert L. de Groot; John B. C. Findlay; Herman J. C. Berendsen; Andrea Amadei (J. Comput. Chem., 1997)

LINCS: A linear constraint solver for molecular simulations. - Berk Hess; Henk Bekker; Herman J. C. Berendsen; Johannes G. E. M. Fraaije (J. Comput. Chem., 1997)

Molecular Dynamics Simulations: The Limits and Beyond. - Herman J. C. Berendsen (Computational Molecular Dynamics, 1999)

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. - K. Anton Feenstra; Berk Hess; Herman J. C. Berendsen (J. Comput. Chem., 1999)

Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic ester. - Marc F. Lensink; Janez Mavri; Herman J. C. Berendsen (J. Comput. Chem., 1999)

GROMACS: Fast, flexible, and free. - David van der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E. Mark; Herman J. C. Berendsen (J. Comput. Chem., 2005)

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. - Djurre H. De Jong; Lars V. Schäfer; Alex H. de Vries; Siewert J. Marrink; Herman J. C. Berendsen; Helmut Grubmüller (J. Comput. Chem., 2011)

MPI Parallelization of Innovative DPD Thermostats. - Nicolae Goga; Herman J. C. Berendsen; Svetlana Baoukina; Sunita Andreea Moga; George Dragoi; Anton Hadar; B. Paviloiu (ICHI, 2013)