Herman J. C. Berendsen

Molecular dynamics with coupling to an external bath

In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for stu...

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

GROMACS: A message-passing parallel molecular dynamics implementation

Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry

Abstract During recent decades it has become feasible to simulate the dynamics of molecular systems on a computer. The method of molecular dynamics (MD) solves Newton's equation...

An Efficient, Box Shape Independent Non-Bonded Force and Virial Algorithm for Molecular Dynamics

A notation is introduced and used to transform a conventional specification of the non-bonded force and virial algorithm in the case of periodic boundary conditions into an alte...

Towards phase transferable potential functions: Methodology and application to nitrogen

We describe a generalizable approach to the development of phase transferable effective intermolecular potentials and apply the method to the study of N2. The method is based on...

GROMACS: Fast, flexible, and free

Abstract This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the...