The GROMOS96 benchmarks for molecular simulation Original Research Article

A set of biomolecular systems is presented, which can be used to benchmark the performance of simulation programs and computers. It is applied, using the GROMOS96 biomolecular simulation software, to a variety of computers. The dependence of computing time on a number of model and computational parameters is investigated. An extended pair list technique to select non-bonded interaction pairs and long-range interactions is shown to increase the efficiency by a factor 1.5 to 3 when compared to standard procedures. The benchmark results can be used to estimate the computer time required for simulation studies, and to evaluate the efficiency of various computers regarding molecular simulations.