The phrase "to run the simulations" means to use a computer program or model to create and test different scenarios or situations in order to see what might happen. Full definition
A second theory proposes that sleep allows the brain to run simulations of fighting, problem solving, and other key actions before testing them out in the real world. (discovermagazine.com)
To test the validity of the model, the scientists ran simulations using data from a second group of 120 MS patients. (sciencedaily.com)