[gmx-users] Interpretation of g_hbond results

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 24 17:14:47 CET 2009


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?



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


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