[gmx-users] Interpretation of g_hbond results

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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