Do you mean like this
%initializing x,y,t
h=0.1; %step size
t=0:h:50;
x1 = zeros(1,numel(t)); y1 = x1; x2 = x1; y2 = x1;
x1(1)=1;
y1(1)=1;
x2(1)=2;
y2(1)=2;
%value of constants
a=0.1;
b=0.3;
omega=4;
Cnp=0.2;
G=1;
%ode
p=@(x1,y1,x2,y2) (a-x1^2-y1^2)*x1-omega*y1+G*Cnp*(x2-x1);
q=@(x1,y1,x2,y2) (a-x1^2-y1^2)*y1+omega*x1+G*Cnp*(y2-y1);
%loop
for i=1:(length(t)-1)
k1=p(x1(i),y1(i),x2(i),y2(i));
l1=q(x1(i),y1(i),x2(i),y2(i));
k2=p((x1(i)+(h/2)*k1),(y1(i)+(h/2)*l1),(x2(i)+(h/2)*k1),(y2(i)+(h/2)*l1));
l2=q((x1(i)+(h/2)*k1),(y1(i)+(h/2)*l1),(x2(i)+(h/2)*k1),(y2(i)+(h/2)*l1));
k3=p((x1(i)+(h/2)*k2),(y1(i)+(h/2)*l2),(x2(i)+(h/2)*k2),(y2(i)+(h/2)*l2));
l3=q((x1(i)+(h/2)*k2),(y1(i)+(h/2)*l2),(x2(i)+(h/2)*k2),(y2(i)+(h/2)*l2));
k4=p((x1(i)+k3*h),(y1(i)+l3*h),(x2(i)+k3*h),(y2(i)+l3*h));
l4=q((x1(i)+k3*h),(y1(i)+l3*h),(x2(i)+k3*h),(y2(i)+l3*h));
x1(i+1) = x1(i) + h*(k1+2*k2+2*k3+k4)/6;
y1(i+1) = y1(i) + h*(l1+2*l2+2*l3+l4)/6;
x2(i+1) = x2(i) + h*(k1+2*k2+2*k3+k4)/6;
y2(i+1) = y2(i) + h*(l1+2*l2+2*l3+l4)/6;
end
%draw
plot(t,x1,'r',t,x2,'y')
xlabel('t','fontsize',14,'fontweight','bold')
ylabel('x1 & x2','fontsize',14,'fontweight','bold')
set(gca,'Color','k')
legend('x1','x2','TextColor','w')
figure
plot(t,y1,'r',t,y2,'y')
xlabel('t','fontsize',14,'fontweight','bold')
ylabel('y1 & y2','fontsize',14,'fontweight','bold')
set(gca,'Color','k')
legend('y1','y2','TextColor','w')
