>Mark, > >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! > >Regards, >Sung
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! Sung _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php