[gmx-users] What is the autocorrelation time

[Erik Marklund]

Dear Chris,

As I see it there one can interpret the acf and correlatation time further for certain types of data. I'll use the h-bond autocorrelation function as an example. Here the data is time series of logical true and false, represented as ones and zeros. This type of acf can be direcly interpreted as a probablity, and some quantities derived from the acf can bear further meaning because of this.

I also thought that the nature of the data may be such there is a non-exponential part, which makes the autocorreltaion time less valid, or less connected to other intuitive concepts. Again, the h-bond acf has distinct features which are non-exponential and the autocorreltaion time derived from such acfs may in fact be misleading when the h-bond kinetics is to be determined.

Hope that makes sense. I's be happy to hear from you if you disagree.

Best,

Erik

19 maj 2012 kl. 04.01 skrev Christopher Neale:

> Dear Erik:
> 
> I thought about your comment for a while and I have come to understand that you are correct. The exponential (or integral) autocorrelation time is a mathematical construct and is defined as such. What I was looking for was an interpretation of the autocorrelation time in terms of the time required to decorrelate the sampling.
> 
> As to whether or not this will depend on the nature of the data, I don't really understand your conjecture. If the interpretation of the autocorrelation time depends on the nature of the data, then that implies to me that a single scalar value is useless in this case. I don't understand how it could be useful to represent the autocorrelation time by a single number if that number does not mean anything on its own. If you have time, I would appreciate if you could elaborate on this point.
> 
> Thank you,
> Chris.
> 
> -- original message --
> 
> Aren't you looking for an interpretation rather than a definition? And will this not depend on the nature of the data?
> 
> Best,
> 
> Erik
> 
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120520/53c14bae/attachment.html>