[gmx-users] Autocorrelation function

[sun]

Hello
I have completed a protein ligand MD using Gromos43a1 and Gromacs v 5.0. I want to know while using gmx analyze, autocorrelation graph between eigenvectors is generated. However, the value is going sharply down to 0 and then to negative values. This probably means that something is wrong with the simulation. I want to assess the stability of helical conformation in the presence of ligand. 
Secondly, I want to know what is exactly the meaning of following line:
Option -ac produces the autocorrelation function(s). Be sure that the time interval between data points is much shorter than the time scale of the autocorrelation.

Please someone elaborate.
With Regards
Suniba

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