[gmx-users] Interpretation of g_hbond results
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 25 00:28:06 CET 2009
David van der Spoel wrote:
> Justin A. Lemkul wrote:
>> 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
> 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?
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users