Use a temporary variable:
for a=[1:100];
%coding here left out
FMJ_cars_wait_2 = @(T12,MJ_V12) (lambdaMJ_sec(a) - MJ_Flow);%
[T12,temp_var] = ode45(FMJ_cars_wait_2,[MJ_Red,Total_cycle],R_G_MJ);
MJ_V12(:,a) = temp_var;
end
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