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.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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