The SNARE protein complex is central to membrane fusion, a ubiquitous process in biology. Modelling this system in order to better understand its guiding principles is a challenging task. This is mainly due to the complexity of the environment: two adjacent membranes and a central bundle of four helices formed by vesicular and plasma membrane proteins. Not only the size of the actual system, but also the computing time required to equilibrate it render this a demanding task requiring exceptional computing resources. Within the DEISA Extreme Computing Initiative (DECI), we have performed 40 ns of atomistic molecular dynamics simulations with an average performance of 81.5 GFlops on 96 processors using 218 000 CPU hours. Here we describe the setup of the simulation system and the computational performance characteristics.