From: Laercio Pol Fachin <[EMAIL PROTECTED]>
Date: September 30, 2008 9:50:48 AM EDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Hydrogen Bond Lifetime
Reply-To: [EMAIL PROTECTED], Discussion list for GROMACS
users <gmx-users@gromacs.org>
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?
Hi,
The HB definitions and associated lifetimes are a bit arbitrary, so
there' s always going to be some ambiguity here. That being said,
the reason the integral of the HB correlation function C(t) isn't an
ideal definition is that C(t) is only roughly exponential. Same
argument goes for getting the lifetime from a fit to C(t), or looking
for the time where C(t)=1/e, or similar simple approximations.
What Luzar recommends is to think about an equilibrium between bound
and unbound molecules, so that they interact with a forward and a
backward rate constant k and k'. k gives the forward rate, ie. the
HB breaking rate, and k' gives the HB reformation rate... they are
not equal due to the diffusion of unbound molecules away from the
solvation shell. There are a few advantages of going this route, not
the least of which is that you tend to get similar lifetimes
regardless of small changes in the HB definition, and whether you use
geometric or energetic criteria, etc.
Extracting these rate constants is a bit tricky (I usually do it by
hand), but I guess gromacs has a scheme to do it... I haven't
actually looked at it (though I really should!). I'd recommend some
caution though, a scheme that works well for HB's between water
molecules in bulk may need to be adjusted to properly model HB's
between water and polar atoms.
So in this case, the "best" rate constant is probably 0.797 ps-1 or a
time of 1.254 ps, which is only a bit slower than in bulk water. I'm
very surprised that the backward rate constant is so small though...
this is about 1 ps-1 in bulk water! I've never seen k' be this small...
Exhaustive details about the HB dynamics issues can be found eg. here:
A. Luzar, JCP 113, 10663 (2000)
Hope this helps,
Chris Daub
(currently postdoc with Dr. Luzar).
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