You can rewrite the code in this way:
F=13.4;
a=0.1;
fun=@(x,t) dfile(x,t,F,a);
[t,x] = ode45(fun,[0,20],[0;0]);
plot(t,x(:,1))
title('nonlinear')
xlabel('t'), ylabel('y'), grid
function xprime = dfile(t,x,F,a)
xprime = zeros(2,1);
xprime(1) = x(2);
xprime(2) = F*cos(t) - a*x(2) - x(1)^3;
I define the function handle of dfile out of the ode45 function. In this way you can pass the parameter to the function.
Now you can make a for cicle to make different plots, for example:
F=[12.3 13.4];
a=[0.2 0.1];
for i=1:length(F)
figure();
fun=@(x,t) dfile(x,t,F(i),a(i));
...
end
I add the function figure() so that plots on different figures.