[gmx-users] Interpretation of g_hbond results

[Justin A. Lemkul]

Manik Mayur wrote:
> 
> 
> On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> 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:
> 
> 
> Which paper are you talking about? Is there a paper for each gromacs 
> postprocessing tool?

Look for this type of information in the output (either to screen or to logs in 
the case of mdrun):

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------

I don't know if there is a paper for every single tool, but pertinent algorithms 
are cited when necessary.

-Justin

> 
>     --------------------------------------------------
>     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
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> -- 
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
> 
> 
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-- 
========================================

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

========================================