Classical molecular dynamics

The special issue of the Journal of Chemical Physics (JCP) highlights developments in and applications of classical molecular simulation. The present issue includes discussion of some of the major software packages for classical molecular dynamics (MD), including Amber, CHARMM, GROMACS, LAMMPS, and NAMD. But even more attention is given to development of underlying models and algorithms. A number of articles in this special issue report recent algorithmic implementations and advances in performance of commonly used MD engines on modern hardware architectures on graphical processing unit (GPU)-accelerated hardware architectures. These include a detailed survey of features and capabilities and recent GPU acceleration of NAMD, a review of major algorithmic advances in GROMACS focusing on taking full advantage of GPU acceleration, implementation of GPU-accelerated Martini coarse-grained simulations in ddcMD, and parallel implementation of hyperdynamics in LAMMPS to perform accelerated MD simulations for solid-state systems.