There are so many issues. Let's address your error first. Your counter variable n is bigger than the size of your y vector (on this line, Yv=(y(n+1)-(y(n)))/0.0005;). Hence you get the error.
Nevertheless you don't really calculate velocity. You simply initialize v vector with zeros and and trying to calculate only one element (because m is just 1 and you don't have a loop to calculate the other elements).
If you want to carry out your calculations with a loop (Matlab is much more powerful, no loops are needed for your problem though), simply use one loop with a counter variable like below.
your constants here
numOfElements = numel(Theta);
y = zeros(1,numOfElements);
v = zeros(1,numOfElements);
for count = 1:numOfElements
y(count) = something like a*theta(count)*bla*blabla
v(count) = something else