A trajectory of 1 ns simulated with a 2 fs time step, and with coordinates saved every 500 steps (NSAVC 500 in the dynamics command) will contain 1000 frames (1000*0.002ps*500=1000ps=1ns).
If you read this trajectory with NSKIP 2500 only every fifth frame (ie, every 5ps) will be read.
NCORS is the number of points in the MSD(t) curve.

For the above trajectory the NCORS 100 and NSKIP 1000 would compute MSD(t) from t=0 to t= 100 * 1000 * 0.002ps=200ps

You have to compute MSD(t) to a large enough t that you clearly see the linear part. Using a small NSKIP increases the computational time, but this is usually not a problem.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden