You can create a matrix where you take every 100 consecutive samples of your waveform and use those as the columns of the matrix. The you can compute the RMS value for each column.
x = randn(1e6,1);
for nn = 0:1e4-1
X(:,nn+1) = x(nn*100+1:(nn+1)*100,1);
end
You could also try repmat for this, but you may run into memory problems.
x = randn(1e6,1);
x1 = repmat(x,[1e2 1e4]);
The for loop above should not have memory issues.
