I'm not sure why colormap is in there--you can remove that line.
Set the y axis limits like this:
ylim([3000 8000])
Set the color axis limits in a similar way to make sure the colors change with the data like this:
caxis([150 575])
where I've used 150 and 575 as some arbitrary low and high values.
Try to do as little as possible inside the loop, because every time you call something in a loop, it eats up computational time. I suggest this rewrite:
h = surf(P_overtime(:,:,1));
axis tight
colorbar
ylim([3000 8000])
caxis([150 575])
for n = 2:N;
set(h,'cdata',P_overtime(:,:,n),'zdata',P_overtime(:,:,n))
drawnow
pause(.2)
end
