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).
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.
Cheers,
--
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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