[gmx-users] Hydrogen bond autocorrelation function (HBAC)
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 22 16:21:02 CEST 2003
On Wed, 2003-10-22 at 16:02, Ester Chiessi wrote:
> Hi.
>
> 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?
>
I'm actually working on a manuscript with this stuff. It is not trivial.
Interpretation depends on a physical model, like a discrete number of
events each with their own time constant. Some people define a time
constant t from C(t) = 1/e
The integral of C(t) can be quite generally be described as the
"correlation time". Just integrate in xmgrace. If you have better/other
ideas please let me know...
Furthermore I have almost completely rewritten the g_hbond program for
my analyses, mainly because in g_hbond 3.1.4 all D-H A triplets are
treated as a different hydrogen bond. In the new code one can choose to
use that, or to merge the hydrogen bonds with the same D-A but different
H into one, which gives longer lifetimes. (e.g. for water-water there
are four possible hydrogens).
This new code is in the CVS version.
> Thanks
>
> Ester
>
> 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)
> http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
> e-mail: ester.chiessi at uniroma2.it
> Phone: 39*6*72594462
> 39*6*72594874
> Fax:39*6*72594328
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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