David van der Spoel
Molecular Biophysics Group
Department of Cell and Molecular Biology
Uppsala University
Classical molecular dynamics (MD) simulations describe the motion of molecules as a function of time based on simple physical models. From these trajectories many physical and chemical observable can be derived.
MD calculations form a demanding application for HPC systems for the counter-intuitive reason that the computational demands are low - per time step. Since however, many sequential time steps are needed (> 1e9) it is difficult to obtain very fast simulations by parallellization alone. Ways to optimize simulation output per CPU cycle will be discussed.
Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theor. Comp. 4 pp. 435-447 (2008) http://dx.doi.org/10.1021/ct700301q