[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:
>> 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,

> Cheers,


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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