archlinux - Arduino + 3 step motors with a bipolar steppermotor controllor

Hallo First of all I am useing archlinux and the mablab support package from http://www.mathworks.se/matlabcentral/fileexchange/32374 So for our university project we have to make a robotic arm which has to move en the 2D plane and rotate about it's own axis - We are confined to by the university to do this with an arduino and step motors and they prefer we program it all in MATLAB - I am using a bipolar steppermotor controllor to control the stepmotors, individually it is working fine, but I can't get them to run simultaneously and at this time I haven't been able to figure out the code to use - the code i am useing now is:

step=1800; %1800 steps

for i=1:step

a.digitalWrite(13,1);

pause(0.001)%Pause is neassesary not to stall step motor

a.digitalWrite(13,0);

pause(0.001)

end

What I was thinking might work is

tic

while toc/30<1

step=1800; %1800 steps

for i=1:step

a.digitalWrite(13,1);

pause(0.001)%Pause is neassesary not to stall step motor

a.digitalWrite(13,0);

pause(0.001)

end

end

while toc/60<1

step=1800;

for i=1:step

a.digitalWrite(8,1);

pause(0.001)

a.digitalWrite(8,0);

pause(0.001)

end

end

But this is not working like I had hoped. Hope anyone has an idea that can help me :)