<br><br><div class="gmail_quote">On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Hi,<br>
<br>
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:<br>
</blockquote><br>Which paper are you talking about? Is there a paper for each gromacs postprocessing tool?<br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
--------------------------------------------------<br>
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2<br>
Forward 0.003 309.475 19.590 0.000294756<br>
Backward 0.007 136.034 17.471<br>
One-way 0.002 471.990 20.678<br>
Integral 0.001 1534.894 23.717<br>
Relaxation 0.002 606.619 21.325<br>
<br>
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?<br>
<br>
Thanks,<br>
Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>