[gmx-users] Hydrogen Bond Lifetime

Laercio Pol Fachin laercio_pf at yahoo.com.br
Tue Sep 30 15:50:48 CEST 2008

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?

Thanks in advance,
Laércio Pol-Fachin

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