[gmx-users] Hydrogen bond autocorrelation function (HBAC)

Ester Chiessi ester.chiessi at uniroma2.it
Wed Oct 22 15:43:01 CEST 2003


I found the following message (dated 14 Apr 2003) in the mailing list
archive, but I couldn't find any answer.
Now, I'm looking for just the same informations.
Please, could you give me any suggestion?



Senthil Kandasamy wrote:

> I have a few questions about the hydrogen bond autocorrelation function.
> While using g_hbond with the -ac option, the relevent output is
> hbac.xvg. "xmgrace -nxy hbac.xvg" shows two lines: one of them is the
> actual autocorrelation function (the one that decays from 1 to zero
> asymptotically and shows fluctuations. ) What exactly is being plotted
> as the other line? (the smoother one which looks like a simple
> exponential fit). Is it just the fit?
> Also, the manual (ver 3.1.1, pg 160) says that a simple estimate for the
> H-bond lifetime can be obtained from the integral of C(tau). It also
> says that a more-sophisticated analysis can be used to get better
> estimates for the H-bond lifetime using multi-exponential fits. I have
> seen some papers in the literature which estimate these lifetimes using
> multi-exponential fits, but am not convinced about the validity of some
> of the methods used. Let's say, I fit the HBAC as a sum of three
> exponentials
> y=a0*exp(-t/a1) + a2*exp(-t/a3) +a4*exp(-t/a5)
> and I estimate a0 through a5, how would I get a good estimate of the HB
> lifetimes from these values? I have seen some papers just average out
> the three timeconstants (a1+a3+a5)/3. I am not totally convinced by it.
> Is that a valid way to calculate a lifetime?
> I would appreciate it if anybody would throw some light on this and
> explain how "a better estimate of hydrogen bond lifetimes can be found
> using multi-exponential fits".
> Thanks.
> Senthil
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Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462

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