Laercio Pol Fachin wrote:
Hi, all.

I am analyzing the hydrogen bond lifetime of water molecules around polar atoms of my molecule. However, I have faced different HB lifetime definitions in different sources. A sample of what I obtained employing g_hbond is below:

"g_hbond -f .xtc -s .tpr -n .ndx -ac .xvg -b 0 -e 10000"

Type      Rate (1/ps)  Time (ps)  DG (kJ/mol)
Forward         0.797      1.254       5.089
Backward        0.061     16.475      11.474
One-way         1.323      0.756       3.835
Integral        0.948      1.055       4.661
Relaxation      2.195      0.456       2.579

# In GROMACS 3.3 manual, page 171, it is said that "the integral of C(t) gives a rough estimate of the average H-bond lifetime", which points to a HB lifetime of 1.055 ps (right?); # On the other hand, in previous discussion in this list, I have found that "according to Luzar the time corresponding to the forward rate constant should be regarded as 'the' hbond lifetime", which points to a HB lifetime of 0.797;

Can anyone please clarify such points?
@Article{ Luzar2000a,
  author =       "A. Luzar",
  title =        "Resolving the hydrogen bond dynamics conundrum",
  journal =      BTjcp,
  year =         2000,
  volume =       113,
  pages =        "10663--10675",
}
@Article{ Spoel2006b,
  author =       "D. {van der Spoel} and P. J. {van Maaren} and
                  P. Larsson and N. T{\^i}mneanu",
  title =        "Thermodynamics of hydrogen bonding in hydrophilic
                  and hydrophobic media",
  journal =      BTjpcb,
  year =         2006,
  volume =       110,
  pages =        "4393-4398"
}




Thanks in advance,
Laércio Pol-Fachin


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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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