On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul <[email protected]> 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? -------------------------------------------------- > 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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur
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