David van der Spoel wrote:
Justin A. Lemkul wrote:
Hi,
I have a quick question about interpreting the output from g_hbond. I
am using the -ac option to calculate H-bond lifetimes between my
protein and a series of different, bound ligands. I read the
associated paper, but I would like to confirm the interpretation of
the results before I continue much further. I obtained the following:
--------------------------------------------------
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.003 309.475 19.590 0.000294756
Backward 0.007 136.034 17.471
One-way 0.002 471.990 20.678
Integral 0.001 1534.894 23.717
Relaxation 0.002 606.619 21.325
The "forward" and "backward" rates and times make sense based on
equations 3 & 4 in the paper, but I could not find an explanation of
what "one-way" and "relaxation" are. Is the "integral" value taken
from equation 2, and thus should be interpreted as the overall H-bond
lifetime?
Thanks,
Justin
One-way assumes k' (Backward) rate is zero, Relaxation is the time at
which C(t) = 1/e
Integral is just the integral of C(t), which in case of exponential
relation should be the same as the relaxation time (not very close as
you see).
Thanks, that makes sense. According to the terminology in your paper, then, if
k is the rate constant for HB breaking ("forward"), then 1/k is the lifetime of
the hydrogen bond. So that lifetime would be the time (in ps) given in the
"Forward" entry? It seems simple, I just want to be sure since there are a
couple of old threads in the archive where users claimed that "Backward" was the
value to use.
Two caveats: first, we recently found out that the numbers in my JPCB
paper can not be reproduced in 4.0 (embarassingly this was found out
during a tutorial that I was giving). We are looking into this. Second
we are busy implementing a new algorithm due to Markovitch * Agmon (JCP
129 (2008) p. 084505) that has several advantages over the Luzar approach.
My simulations were conducted under 4.0.2, should I not use these results?
Results from 3.3.x should be correct, since it was used in your JPCB paper; but
my installation of 3.3.3 gives a segmentation fault on our cluster, and a bus
error on my local machine. Are there known issues with g_hbond-3.3.3?
Or should I just hold off and do analysis after a new version comes out and
these issues are solved or a new algorithm implemented?
Thanks again,
Justin
Cheers,
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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