[gmx-users] Hydrogen Bond Lifetime
Laercio Pol Fachin
laercio_pf at yahoo.com.br
Tue Sep 30 15:50:48 CEST 2008
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,
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