[gmx-users] autocorrelation function using g_analyze

Sung Hyun Park parksh at northwestern.edu
Fri Sep 18 22:29:00 CEST 2009


Does anyone know exactly how g_analyze -ac calculates autocorrelation function?
My input file, dist.xvg, contains a distance d(t) between two specific
atoms of my molecule in time t. (hence d(t)>0)
I calculated the autocorrelation function using the following command:

g_analyze -f dist.xvg -ac corr-dist.xvg

What I don't understand is that the correlation function C(k) in the
output file, corr-dis.xvg, includes some negative values and even goes
down to almost -0.5!
I thought by definition the autocorrelation function C(t) is
calculated as following:

C(k) = <d(t)*d(t+k)>

where C(k) should be always positive because d(t), distance, is always
positive in this case.
So does anybody know precisely what formula "g_analyze -ac" uses to
calculate the autocorrelation function?

Thank you very much for your help in advance.


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