[gmx-users] Re: Re: Re: autocorrelation function using g_analyze

Sung Hyun Park parksh at northwestern.edu
Mon Sep 21 18:39:46 CEST 2009

>Thank you for the reply.
>However it is not the definition of the autocorrelation function, isn't it?
>Autocorrelation function <C(t)> is generally normalized by <C(0)>, and
>eq.(8.9) in the manual can be used to calculate <C(t)>. (please
>correct me if I'm wrong)
>As I mentioned in my original post, the quantity I'm interested in is
>a distance correlation hence I believe the autocorrelation should
>always be positive.
>I just don't see how the autocorrelation function, normalized or not,
>can become negative in my case.
>If gromacs is indeed doing what you suggested (subtract mean from all
>data points, divide by standard deviation), it is not the
>autocorrelation function generally defined by any textbook to my
>knowledge.(again, please correct me if I'm wrong) Furthermore the
>formula you suggested is the correlation of the "fluctuation" of the
>quantity, not the correlation of the quantity itself.
>Do you know why gromacs calculates the autocorrelation function in
>that way instead of using eq (8.9) and normalizing using C(0)? Any
>reference would be also helpful.
>Thank you again for your kind help!

Please disregard my previous post shown above. I understand it now.
Basically my definition and gromacs definition which Mark mentioned
earlier are the same, just a matter of shift by a constant or not.

Justin and Mark, thank you so much again for your help!


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