@Nisar Ahmed, I think what you want to do to have Simulink outputs grouped across multiple runs is something like the example in Run Simulations Programmatically - MATLAB & Simulink (mathworks.com) and the example repeated here where all the outputs from each sim run are collected together in an array of Simulink.SimulationOutput. The loop here could instead not be a loop and just a bunch of manually entered simOut(run) = sim(__) calls after setting your run-to-run model changes:
N = 100;
simOut = repmat(Simulink.SimulationOutput, N, 1);
for i = 1:N
simOut(i) = sim('vdp', 'timeout', 1000);
end