Photoinduced Conformational Dynamics of a Photoswitchable Peptide: A Nonequilibrium Molecular Dynamics Simulation Study

Molecular dynamics with coupling to an external bath

Herman J. C. Berendsen, Johan P. M. Postma, Wilfred F. van Gunsteren et al. · The Journal of Chemical Physics · 1984 · 30.3K citations · Full text

Vibronic Interaction, Thermodynamic Modelling, Engineering +13

Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems

Tom Darden, Darrin M. York, Lee G. Pedersen · The Journal of Chemical Physics · 1993 · 29.8K citations · Full text

Numerical Analysis, Engineering, Electrostatic Energies +18

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

Jean-Paul Ryckaert, Giovanni Ciccotti, Herman J. C. Berendsen · Journal of Computational Physics · 1977 · 21.1K citations

Numerical Analysis, Cartesian Equations, Engineering +11

GROMACS: A message-passing parallel molecular dynamics implementation

Herman J. C. Berendsen, David van der Spoel, Rudi van Drunen · Computer Physics Communications · 1995 · 10.2K citations

Engineering, Parallel Programming, Computational Chemistry +4

GROMACS 3.0: a package for molecular simulation and trajectory analysis

Erik Lindahl, Berk Hess, David van der Spoel · Journal of Molecular Modeling · 2001 · 6.9K citations

Biophysical Modeling, Engineering, Computational Biology +11