Fig. 3.

Strong scaling of medium-to-large systems. Simulation performance is plotted as a function of number of cores for a series of simulation systems. Performance data were obtained on two clusters: one that is thinly connected using QDR Infiniband but not full bisectional bandwidth and a more expensive Cray XE6 with a Gemini interconnect. In increasing order of molecular size: the ion channel with virtual sites had 129 692 atoms, the ion channel without virtual sites had 141 677 atoms, this virus capsid had 1 091 164 atoms, the vesicle fusion system had 2 511 403 atoms and the methanol system had 7 680 000 atoms. See Supplementary Data for details