Re: about Hydrogen Bond correlation function

From: Axel Kohlmeyer (
Date: Thu Nov 04 2010 - 08:59:45 CDT

On Thu, Nov 4, 2010 at 9:11 AM, Hannes Loeffler
<> wrote:
> On Thu, 4 Nov 2010 13:55:28 +0800
> 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.
> I guess what you are asking is whether the angle brackets denote an
> ensemble average or a time average.  But in the context of the paper


> cited above wouldn't you want to average over all water molecules at
> some stage anyway (obviously assuming that all water molecules are
> equivalent)?  In other words, time average or ensemble average first or
> the other way round?  I would think, mathematically speaking, that
> should not make any difference (or am I wrong?).  Eventually, think
> about the situation where you have only a single HB pair.
> Cheers,
> Hannes.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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