Re: about Hydrogen Bond correlation function

From: Chris Harrison (
Date: Thu Nov 04 2010 - 06:49:40 CDT

Dear Jun Zhang,

The specific nature of your system determines which case is best suited for
you. Chandler's paper examines liquid water, in which case it is a system
of homogeneous pairs, and <> over all pairs describes a statistical
microscopic property of the bulk system; in this case it makes sense to
average over all pairs. In the case of a protein system, which
contains heterogeneous pairs that are not a regular lattice, <> over all
h-bond pairs does not seem particularly meaningful. In such an example, you
should most likely restrict <> to a particular h-bonded pair over your
trajectory, unless you are examining for example the water-to-water
h-bonding properties of water solvating the protein.


On Thu, Nov 4, 2010 at 12:55 AM, Jun Zhang <> wrote:

> Hello everyone:
> I would like to calculate the HB correlation function according to:
> c(t)=<h(0)h(t)>/<h>
> in "Nature,379:55-57". However, I have been convoluted by the meaning of
> <>:
> Is it an average over all atom pair at a particular time or over the
> entire trajectory for a particular pair? I prefer the second definition, but
> I am not sure. Please help me. Thank you in advance.
> Jun Zhang
> Nankai University

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078

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